Oh crap, last night I couldn't sleep and I was constantly thinking about my intercooler and plenum changes.
It seems that I have almost convinced myself that I am going to remove my A2W IC barrel from the boot, and start all over again, doing it the way that I should have always done it...like MR2QIK, stuka, dasic1, etc, with a new A2W IC on the left of the engine bay, and a new left-side-feed plenum. Almost everything about this option is better than the other options, except for the fact that I'll be starting from scratch. I think it will be worth it though.
Once the boot is all patched up, I can just treat it as a fresh A2W IC install. I'll have to re-do the air piping, but that's no big deal, and it will be simpler and shorter anyway. The main downside is that I'll have to spend more money to get the new A2W IC, but the PWR barrel was not the best choice in hindsight, so again it's a worthwhile change. The FrozenBoost A2W intercoolers are amazingly good value too, so they look promising for me.