I used the “Wizard” amp sim on the Suite, it’s a very close simulation of the Wizard Modern Classic, a Canadian take on the whole “modded Marshall” thing. It’s my favourite amp sim to practice and record with. For convenience, I didn’t use any external IRs, I used the matching cab provided in the Suite.
The whole thing was boosted with the Mercuriall Greed Smasher, a very accurate emulation of the Mesa Boogie Grid Slammer. It’s an overdrive with a lot of character in my opinion and quite versatile.
On this particular signal chain I didn’t have to remove any Bass, I set it at 4.5-5, that’s the good thing with modded Marshalls even in an amp sim format, they don’t have those bass “farting” issues.
Of course all this is my aesthetic on the whole “hot rodded rock tone” thing. It’s quite unforgiving as you noticed and this is probably why I think I suck all the time! 
Unfortunately I’m not a good DAW editor, so I can’t really manipulate the takes in that way, but we could always keep the best of the two and record a new one when you’re back from your break from all that recording madness. By the way, recording two takes on this is insane and fantastic at the same time.