I've been working on both my GTXs with performance enhancement issues since May. I bought them last year a 96 and a 97. Built the engine on the 97 from parts off ebay.... replaced everything. 96 had no fire issues and MPEM problems.
Rebuild carbs on both skis then did it again and apart for checks, more cleaning.... reset pop off to different settings, etc. I was almost ready to rejet the 96. Here is what I'd do. If you are sure you have mikuni needle and seats and diaphragm and all the good parts in the carbs..... I know you know about the 3 holes in the barrel.

Install slotted rave valves (I machined my own slots in my raves) and buy "new" upgraded valve bodies. A little information on the problems I was experiencing.....After all the work I did to both skis, the 97 still had acceleration issues, a flat "smoke a cigarette and get back to you" attitude from 2500 to 5 or 6K, then came on like a raped ape. I raced my wife often on the 96. I'd jump out to lengths and stay there till she hooked up and drove by me. Her's is faster top end but I just built the engine. The 96 was the smoothest with regard to transition RPM. Had I not had the 97 I would have figured the 96 was pretty darn good. On the speed difference 2-3mph on the GPS I refuse the resort to cheating to make my ski faster.

That said... after the rave valve work she told me her ski didn't come on as hard at 6K. We lined up for a race.... she pulled way from my ski from the start and walked off into the distance. I couldn't get a sniff. I have not rode her ski but judging by what happened, her flat spot ain't flat no mo. LOL Someone on the forum posted about a technical service bulletin to do what I did for customers complaining about a flat spot or hesitation on the 97 models. Give that some due diligence. Good Luck.