How do the plugs look? Is it completely back to stock? Ie. 15 pilots turned to 3 turns out. 100 main jets with no shims. Completely closed airbox with snorkle with stock OEM filter? Stock slide springs? 5 degree timing advancer OFF? It might actually be worth it to take to a shop with a dynometer and get them to tune it. THere is a shop in Toronto that for $300 will dynotune a carbbie bike with unlimited dyno pulls and tuning until the bike is perfect. Do you have such a shop in your city? It might be worth the few hundred bucks to have it running perfectly with the stage 2 I imagine in the states would be slightly cheaper. A dyno run with a fuel/air map and someone tuning it would be foolproof as the dyno and A/F mixture ratios don't lie. If you're using the 17.5's as pilots it will be 1 1/2 turns lower than the equivilent on the 15's. Ie 3.5 turns on the 15's are only 2 turns on the 17.5's. THe same shop does 3 pulls for 50 bucks with printout if you know how to read the fueling or just post it here so we can have a look.
Maybe a stage 1 would be better. Its less of a change from a full blown stage 2 but still gives most of the stage 2 power without being as finicky to temperature/humidity changes. Since you already bought the stuff from Holeshot to go to a stage 1 you would just need $8 in jets and go with 110 mains and 15 pilots out to 3.75 turns and a 1.5" hole in the top of the airbox cover and stock filter. You already have the advancer.
The only other thing I can think of is maybe the 5 degree advancer is too much for your specific bike. I've read a guy who did a stage 1, etc ,etc and it was great however when he put on the 5 degree advancer it ran like crap and could barely idle. There was just something about his bike that hated the extra timing advance. Who knows maybe in the factory the timing plate was drilled slightly larger with the holes and had some more advance than other bikes, his coils were unusually good, etc ,etc. Who knows really but he took the advancer off and it was wheelie city. Since taking off the advancer only takes 15 min it might be worth putting the bike completely to stock then starting one step at a time until it starts coming around. If you lean your bike to the left on the kick stand you don't even have to drain the oil. Just put a tinfoil pan underneath the timing signal cover to catch any drips.
I think maybe there was too many drastic steps on the bike than it could take at one time and most of the time on these kits its fine however every bike is different so starting from stock and working up one at a time is a good idea. Here is the stock and other settings for reference in case you need the info:
GEN2/GEN3
Float height 13mm for all
Totally stock:
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Shit stock exhaust
Totally enclosed airbox with stock filter
100 mainjets
15 pilots jets with 3 turns out on mixture screws
Slightly modified for a slip on:(My friends runs great like this)
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Aftermarket slip on, ie holeshot, muzzy, yoshimura, etc ,etc,
102.5 Mainjets
1 Radioshack shim .020 or about 2 of the Holeshot shims
15 pilots to 3 - 3.5 turns out(can't remember think it was 3.25)
Stock airbox with snorkle and stock filter(no extra holes in airbox)
Stage 1:
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Aftermarket slip on, ie holeshot, blah blah
110 Mainjets
2 Radioshack shims or 4 or 5 Holeshot shims
15 Pilots at 3.75 turns out
Stock airbox with snorkle and a 1.5" hole cut into the top
With these baseline settings it should get your pretty close. Since you already have most of the good components of the holeshot kit, ie adjustable needles, etc. It will probably be actually easier to go up a step at a time. If you still have the slip-on on there with the stock settings it will be weird past 1/4 throttle because of the fact that the stock jetting is already lean as hell and making the bike flow better only aggravates it even more. Since you have the good Holeshot needles are you using them? If so where is the C-clip set to? I imagine if you used the Holeshot needles you probably set them to the middle or neutral position. Anything over 1/4 throttle to 3/4 of a throttle is adjusted by the needle. Even with the stock jets, the bike might run better if you richen up the needle a notch by putting the c-clip down a notch or two. That and maybe turn the mixture screws out a 1/4 turn to 3.25 might do the trick for now. Since this is a small step you will be able to feel the improvement right away.
Although looking again at your symptoms it seems like you have a fuel starvation problem. Have you tried running the bike on prime? When you ride around for a bit, pop the gas cap off. Do you hear a whoosh?? You could try running with the gas cap loose to see if you have the breather hole grundged up. Carbs very very very rarely just stop functioning. Even crazily out of tune, they should work sufficiently to run the engine through the rpm ranges. Try the petcock first as that is usually the culprit with fuel feeding problems, either too much or too little fuel.
If you wanted to try this as well. Run the bike till its warm and take off the tank. Attach a funnel to the fuel line and plug the vacuum tube that goes to the #4 carb with a screwdriver bit or a piece of tape. Have a little bottle of fuel so you can sort of top up the funnel with fuel so you can run the bike without the tank off it. Does the bike run better?(don't drive it just rev it) Does it suddenly have a more snappier throttle? If so the petcock might be wonky. While the tank is off, does the spigot leak when the bike is on "ON" or "RESERVE"? Does the fuel flow freely when set to "PRIME"? It could be that the diaphram is dead on the petcock or gummy and the vacuum from the bike running only can move it so far to provide a limited amount of fuel.