When I acquire a spawner for a mob farm, I tend to add a comparator, wool, chorus fruit, dragon egg/soul lantern, and reduce the min delay with sugar and sometimes clocks for max delay. The enderio spawners in that huge list and the ones from Pneumaticraft aren't as flexible as the vanilla+apotheosis variants. So focus on the apotheosis variants that require silk touch or a cardboard box. The spawner scrap needed to upgrade the forge in Forbidden and Arcanus can be collected from "junk" spawners being broken with a pickaxe (without silk touch, of course). Of special note are the evoker fang spawners in some caves. They are the best spawners to find as the min and max spawn delays are minimal already. You will be able to change the mob in the spawner with a spawn egg. The capturing enchantment, once applied to your sword, will be great for acquiring the spawn eggs. The spawner modifications that include the nether quartz in the offhand, are for inverted adjustments of the same type. You'd use this to reduce spawn range, for example, to fit the radius of your mob farm if the spawner radius is too big. Redstone link (from create) is my method of turning my mob farms off/on wirelessly. Remote lever from cyclic seems to be similar in function with just a vanilla lever and the device (OMG this thing is cheap). Additional note: redstone carries through spawners, so a lever or link on a side will pass through signal to adjacent spawners. This means the 5 other sides of the central spawner can activate connected spawners at the same time. A room with a 9x9x9 space inside (11x11x11 externally) will handle them without spawning mobs outside the box. Spawn radius should be verified to be 4 on these guys. Apotheosis enchanting will be your best route to acquire some really high powered enchantments and is well worth your time to get setup. Silk touch a HUGE stack of bookshelves in preparation for this! The advanced enchanting infuser coupled with this setup will allow you to choose the enchantments you add. You asked how to make a "soul vial", though this isn't the use case you want them for, you'll want them for making various enderio items in the future: make the empty soul vial, place it in your main hand and right click the target mob or villager. Boom. Done! To make grains of infinity, take a flint and steel to bedrock and light the bedrock on fire. When the flames die, there's a chance to spawn the grains. In the future, consider turning on subtitles as they pop up with a direction (if not directly in front or behind you) to help you find the source of a sound. The sound muffler is worth learning to shut off distracting noises. Make and open those loot bags!!! There are pressies to be claimed. As for building with gaps: I don't think it's worth the effort as wireless options exist in the modpack for power, fluids, items, etc. Though, having specific layers of ceiling and flooring will make adjacent floors not have unsightly piping peeking through. A 1 block tall gap can still spawn spiders if there's a 3x3 space available. So, back to bedrock level stuff, and once you have redstone being generated in quantity, you can begin wireless power with the Flux Networks mod. Step one is to get yourself at least 24 stacks of redstone dust. 8 stacks can be converted to flux dust in a single go (consuming a single piece of obsidian in the process as it gets turned into cobblestone). The JEI for flux dust is rather unique. The basics are expose bedrock (corners are great for this exercise), throw down 8 stacks of redstone onto the single corner block. Place a piece of obsidian over it (1-block gap only). Then left-click (punch) the obsidian. It smashes the redstone into an equivalent amount of flux dust. I recall doing this process twice in my playthroughs (48 stacks). The flux points and plugs you'll use to connect generators and machines require the stuff. Light level overlay can be toggled off/on with F7. Don't leave it on! Feral flare lantern places lights but can interfere with multiblock structures that include a gap in them. I tend to prefer these to mega torch as the mega torch can stop stuff from spawning. And to really let mobs know to keep away from me, I use an interdiction torch (or 3). I have avoided commenting on your storage setup as I feel you need some more basic resources to get started. There are these mods available in this pack that i recognize: ars nouveau, tom's simple storage, integrated, pretty pipes, occultism, refined storage and ae2 storage (with 726 mods, i have likely missed some options. lol). While tom's or ars may help out for now, they don't offer advanced auto-crafting which is crucial if you want progress before you turn 100 years old. I use occultism for early storage as I can connect it via a storage bus to ae2 or refined storage once I get around to setting that up (and it's the same basic rituals for making marid crushers (that'd be the 6x ore multiplier)). For auto-crafting, I can only recommend ae2. While refined storage is nice and considered by many to be simpler, it doesn't offer the simplicity of ae2 in many modded device setups. The AE2 extension mods in this pack are amazing.
When I acquire a spawner for a mob farm, I tend to add a comparator, wool, chorus fruit, dragon egg/soul lantern, and reduce the min delay with sugar and sometimes clocks for max delay. The enderio spawners in that huge list and the ones from Pneumaticraft aren't as flexible as the vanilla+apotheosis variants. So focus on the apotheosis variants that require silk touch or a cardboard box. The spawner scrap needed to upgrade the forge in Forbidden and Arcanus can be collected from "junk" spawners being broken with a pickaxe (without silk touch, of course). Of special note are the evoker fang spawners in some caves. They are the best spawners to find as the min and max spawn delays are minimal already. You will be able to change the mob in the spawner with a spawn egg. The capturing enchantment, once applied to your sword, will be great for acquiring the spawn eggs. The spawner modifications that include the nether quartz in the offhand, are for inverted adjustments of the same type. You'd use this to reduce spawn range, for example, to fit the radius of your mob farm if the spawner radius is too big. Redstone link (from create) is my method of turning my mob farms off/on wirelessly. Remote lever from cyclic seems to be similar in function with just a vanilla lever and the device (OMG this thing is cheap). Additional note: redstone carries through spawners, so a lever or link on a side will pass through signal to adjacent spawners. This means the 5 other sides of the central spawner can activate connected spawners at the same time. A room with a 9x9x9 space inside (11x11x11 externally) will handle them without spawning mobs outside the box. Spawn radius should be verified to be 4 on these guys.
Apotheosis enchanting will be your best route to acquire some really high powered enchantments and is well worth your time to get setup. Silk touch a HUGE stack of bookshelves in preparation for this! The advanced enchanting infuser coupled with this setup will allow you to choose the enchantments you add.
You asked how to make a "soul vial", though this isn't the use case you want them for, you'll want them for making various enderio items in the future: make the empty soul vial, place it in your main hand and right click the target mob or villager. Boom. Done! To make grains of infinity, take a flint and steel to bedrock and light the bedrock on fire. When the flames die, there's a chance to spawn the grains.
In the future, consider turning on subtitles as they pop up with a direction (if not directly in front or behind you) to help you find the source of a sound. The sound muffler is worth learning to shut off distracting noises.
Make and open those loot bags!!! There are pressies to be claimed.
As for building with gaps: I don't think it's worth the effort as wireless options exist in the modpack for power, fluids, items, etc. Though, having specific layers of ceiling and flooring will make adjacent floors not have unsightly piping peeking through. A 1 block tall gap can still spawn spiders if there's a 3x3 space available. So, back to bedrock level stuff, and once you have redstone being generated in quantity, you can begin wireless power with the Flux Networks mod. Step one is to get yourself at least 24 stacks of redstone dust. 8 stacks can be converted to flux dust in a single go (consuming a single piece of obsidian in the process as it gets turned into cobblestone). The JEI for flux dust is rather unique. The basics are expose bedrock (corners are great for this exercise), throw down 8 stacks of redstone onto the single corner block. Place a piece of obsidian over it (1-block gap only). Then left-click (punch) the obsidian. It smashes the redstone into an equivalent amount of flux dust. I recall doing this process twice in my playthroughs (48 stacks). The flux points and plugs you'll use to connect generators and machines require the stuff.
Light level overlay can be toggled off/on with F7. Don't leave it on! Feral flare lantern places lights but can interfere with multiblock structures that include a gap in them. I tend to prefer these to mega torch as the mega torch can stop stuff from spawning. And to really let mobs know to keep away from me, I use an interdiction torch (or 3).
I have avoided commenting on your storage setup as I feel you need some more basic resources to get started. There are these mods available in this pack that i recognize: ars nouveau, tom's simple storage, integrated, pretty pipes, occultism, refined storage and ae2 storage (with 726 mods, i have likely missed some options. lol). While tom's or ars may help out for now, they don't offer advanced auto-crafting which is crucial if you want progress before you turn 100 years old. I use occultism for early storage as I can connect it via a storage bus to ae2 or refined storage once I get around to setting that up (and it's the same basic rituals for making marid crushers (that'd be the 6x ore multiplier)). For auto-crafting, I can only recommend ae2. While refined storage is nice and considered by many to be simpler, it doesn't offer the simplicity of ae2 in many modded device setups. The AE2 extension mods in this pack are amazing.
This is a lot to take in...