With the stuff in your sig, you might need a decent tune to solve the issues. the stock puter/programming is decent, but it is adaptive really for a tractability and emissions standpoint. a major reason for the adaptive control is to make up for bad/degrading sensors, tolerances in components, etc (even right off the assembly line, sensors can have a bit of tolerance from one another). But the adaptive strategy is more geared that way and not so much to accomodate mods (as nice as that would have been).
I totally see James' point about messing with the idle set screw, but here is my take: you are far from stock, so stock settings are likely a good bit off. And even on stock cars, by the time they have a lot of miles on them, often factory settings no longer work best.
also, just note and write down what you do - you can always undo what you did (i do this often with motorcycle jetting and tweaks - it is too hard to keep track of what was done with 4 carbs).
I dont know about your FP question. I agree with James, except I have no clue about FMU's and that would need to be considered (i think. LOL).
good luck with it.