It's pretty well thought out, actually...but there is one flaw: Clouds was discontinued some time back, and the best way to deal with that would be to get a third-party version, with Tall Dog's uClouds SE probably being your best bet on availability. This then opens up 10 hp, with a very good suggestion for 8 of those being a Pamela's NEW Workout. This would do quite a bit to address your clocking/pattern concerns, and it would play very nicely with the Varigate 4+. For the remaining 2 hp, given the sort of complex interconnection you're envisioning, I'd strongly suggest a regular multiple module of some sort...buffered isn't necessary, but making sure you can use this a few different ways is. SSSR has one which incorporates a switch to select either 2x4 or 1x8 modes, a function you might find useful.
As for the Intellijel line-in, yes, that'll work fine for incoming line-level audio, but you're going to need the corresponding Audio I/O 1u tile to make use of the cab's line-in and outputs. I would suggest removing the Pedal I/O tiles and the headphone tile so that that can fit, then consider removing the O'Tool and looking at Retro Mechanical Labs' GPI instead; not only would this restore the pedal I/O, but that module features two pedal interfaces, which would be a perfect complement to the Strymon pedals you have. These do require 3.5mm to 1/4" cables, but those are easily obtainable.