My bike is completely stock, so anything i say here is only guessing .
What makes u think the float bowl is emptying too quick? I can't see how the increased airflow you've created could alter the air/fuel ratio that much that you could drain the bowl. The needle and seat setup in the float bowl will easily compensate for the extra fuel you might be using after altering the needle clip height. If the fuel is too low then you may have a partly blocked fuel line or clogged screen in the fuel tank. Maybe check that.
If the carb is getting the fuel ok then what i think may be happening is as the engine comes rapidly off high revs, the mix goes briefly too lean, stalling the engine because the low speed carb circuit (pilot jet inside the float bowl) is too small for the increased air flow at low revs.
I think you need to read the plug color, as you mentioned you were doing, to find out what the high speed circuit is doing (rich or lean or ok). Then the same for the low speed circuit. Drive at high revs for 5 mins, hit the kill switch and pull in the clutch. Pull over and check the plug. From your earlier post it sounds like the fuel is lean, popping and stuttering, You'd expect that after your K&N filter and new pipe. Then drive around for 5 mins at low speed, say less than 3000rpm and stop engine and check plug color.
Another quik test is :When the engine stalls after being
warmed up fully does it restart better by pulling the choke on a bit? If so it sounds like it is lean at low speeds so the rejet of the pilot may be the way to go. Also, can you start the engine from
dead cold without the choke? That could indicate the low speed circuit is too rich.
If you need to get new jets they should only cost a few dollars each, but where you get them from I don't know. May be best to check with a carb or bike shop there. Our bikes use
TK (Teikei) carbs (type=MV30P-1J on mine) that are similar to the carb used on the Yamaha TW200 bikes - but they use a TK MV28 carb. So Yamaha dealers may be a source for parts. There is a US (Ohio?) website,
http://www.endlessjourneycycles.net/ has a few posts about rejetting and general carby stuff. It may be worth ringing this guy for advice based on experience. Otherwise you may just spend a lot of cash and time and end up with a badly running bike.
Re the jet size, should be stamped on the jets, hopefully. May need a magnifying glass. I think someone put a post on this site about the jets but i can't find it.