Sounds like you have gotten on the right track, ill try and share some of my carb tuning experience from my stock 07 yfz. the previous owner had every setting messed up..
Id start with the "mother fcr tuning info thread" if you haven't already found it, I haven't posted enough to be allowed to share links.
Even if you already know what the carb jet components are, the thread explains exactly what each jet circuit controls and some symptoms to recognize when tuning.
Backfiring on decel, or backfiring in general is the easiest way to recognize either the pilot or needle is too lean. If it backfires on a gradual deceleration(not chopping the throttle) then richen the needle. If it backfires on chopped throttle then richen the pilot.
So if you decrease the pilot size from what you currently have, I would expect the backfiring to get worse and it might start having trouble idling. I'd buy the next three sizes up in pilots and start working my way up until the backfiring stops at chopped throttle. with a full pipe system and a built engine, she'll need a larger than average pilot.
Bog at WOT is a sign of being too rich as well, so I would start with that by decreasing the main jet like you mentioned. Buy the next 3 or 4 smaller sizes and start stepping it down until it starts pulling better (it may take smaller sizes than that).
As a side note that I wouldn't worry about until you have it nearly dialed in, there could be some extra power to be had with the perfect main jet setup. Even if your jets are close enough to allow the bike run smooth and pull hard, the main can be altered some to give a few more HP, nothing crazy, maybe 2-4 if you're lucky. when you find the sweet spot that gits rid of the bogging, go up and down a size and see if it pulls any harder at WOT. It's not guaranteed, but worth a shot, these fcr carbs can be picky.
My bike when I bought it looked flawless, but it couldn't idle, ran crappy at half throttle, backfired any time you let off, and had slight bog at WOT lol, I've had the carb off way too many times to count... but I've gotten it nearly dialed in.
Goood luck Man!