Did you check the oil for water contamination and the water level in the radiator?
The stock jets for the low flow head were 45 and 142.5.
If I were you I would install those jets or get as close as you can, bolt on your new muffler and go for a ride...how does it run?
Now adjust the fuel screw for fastest idle, then close it 1/4 turn. Reset the idle to 1500rpm.
Go for a ride, how does it run?
Since you have no snorkle next remove the side cover leaving the air cleaner in place and exposed. Go for a ride.
Does it run differently and or better?
If it does consider enlarging the snorkle hole.
Replace the side cover.
By now the engine should be running perfectly and accelerating cleanly.
Idle should be 1500rpm.
If it isn't concentrate of that problem. Consider the needle position and changing it if the engine is bogging.
Now that the engine runs right if you want to try bigger jets go for it.
Change one jet at a time.
'02 KTM 640 Adventure-lowered
"On the road there are no special cases."
Cormack McCarthy-The Crossing
The faster it goes the faster it breaks.
And high performance=high maintenance.