Motorcycle Repair: my 05 sporty is sick, noticable difference, new spark

Question
Hi Mark, First of all I own a 2005 Sportster XL883C with a little over 30,000 miles on it. I had it parked in the garage for about 10 weeks due to a leave of absence. When I got ready to take her out the battery was dead because I had left the security system armed. I had the battery charged at the local parts house and it fired right up. It drove fine for the first couple of days then all of a sudden it started to spit and cough when I would twist the throttle. After about 2 minutes of embarrasment it finally got a boost of energy and I was able to drive home but at a stop I had to keep the engine revved to about 2000 rpm's . If I let off the throttle   the engine idles ok but coughs if I try to take off. The engine light comes on every now and then along with the alarm light(little red key). At first I suspected bad gas and carb problems. I'm pretty mechanically inclined.... with cars, so I removed the fuel tank and carb. I washed the tank out real good and also replaced the fuel shutoff petcock and screen. I thought maybe it was starving for fuel. I disassembled carb and cleaned it also and installed a stage 1 jet kit that I had in my toolbox for the longest time. I removed the slow and drilled it to .020 & removed the plug for idle mixture screw and set it at two and a half turns to start. I slapped it all back together along with new spark plugs and wires and fired it up. Took it out for a ride and it ran great with a noticable difference. After about fifteen minutes of riding with engine good and hot it did the same thing. Someone advised me to check for vaccuum leaks so the next day I removed intake manifold and the seal on the rear had a small cut and looked like it could be leaking so I replaced both seals including carb seal. Ran great again until it warmed up. If I Iet it cool for awhile it runs great until it heats back up. I'm starting to lean toward ignition problems but certain people don't think so. Could the battery be bad and still crank the engine? Sound crazy to me. Please help. thanks. mdon

Answer
Hey Miguel,

I can see right off the bat, youve done some homework and went for the obvious, I would have said intake seals myself...or bad fuel, but this still doesnt explain why it runs good cold but not warm...So leats eliminate what changes from cold to hot.. Fuel? nope, it may warm with engine temp, but not enough to make the bike run any different. Vaccum? nope. what changes? Well the rubber on the seals will change once its hot (youve done that) ok, the engine needs less fuel when its warm so does the choke make a difference on or off when its hot? i do know ive seen the pick up coil or pulse coil become affected with heat, HOWEVER, they either work or they dont. Could it be electrical? i dont think so... Now as far as the popping out the carb goes, heres what you need to do. Ive done this on alomst EVERY sport or big twin ive touched and they damn near HUG me when im done...
You had the 2.5 turns out right, Get a #45 slow, put the main back to stock (unless you have a big bore, A sporty will never use more fuel than a stock pilot) Put a .30 shim under the slide needle (main jet needle) and VIOLA (vee-oh-lah) lol, given there are NO leaks in the intake seals, this WILL cure the popping issue...You know what youre doing, rule out whats obvious, and go from there...Let me know if any of this helped!

~Mark Panka