Some background on the bike. 99 Sportster XLH1200. Bought the bike about 7 months ago. Put about 5k kms on it. Bike has been abused by previous owner. 55,000 kms on the motor. Issue started after a long day of riding ending with a hill climb on the way home. Bike died and would not start again although it would crank. Pushed it the rest of the way home including an exceptionally brutal hill. Put it on the charger and about 3 hours later it started. Problem didn't happen again for about 2 months. Bike would start in the morning to get me to class then at the end of the day it wouldn't fire. It would crank with some massive backfires when letting go of the start button. Had it towed home. Friend of mine mentioned it may be the kill switch and we thought we figured it out. The bike wouldn't start if you turned it off with the kill switch then tried to start it again but if you turned it off with the key it would fire right up. That worked for a day but then stopped working. Now it won't fire at all. So far I have replaced the battery, ignition module, pickup rotor, spark plug wires, coil. Jumped the kill switch yet it's still not starting. Tested the voltage at the coil. is usually around a half a volt less than battery voltage. Tested the spark with a spark tester and the spark is good and will jump across 1" gap. Took the carb apart and cleaned it out. Checked for gasket leaks. I am at a loss on what to check next. I tried jumping the Bank angle sensor but either I'm not doing it right or that isn't the problem. I'm desperate now as I have spent close to $500 trying to get the bike running .

 

I'm honestly not super familiar with your year sporty but I gotta say if its starting when its cold it sounds like something is getting hot and then failing. Which to me means you possibly just narrowed your problem down to somewhere around the motor. If it was the other way around, I'd suggest to check for intake leaks (like you already did) unless you said you were getting popping out of the exhaust or anything while riding. Anyway...

From across the internet here it does kinda sound like an electrical issue. As in, a bad sensor that creates too much resistance once it gets hot and maybe now has totally **** the bed. Do you have access to a wiring diagram for it? Start with the simple stuff first. Look for a flow chart troubleshooting guide for your year and model with symptom something like "hot-cranks, no start". Prolly will tell you what to check and in what order to narrow down until you find your problem.

I would take out all that jumper wire stuff and put it back the way it belongs before I started diagnosing things too btw.

You can delete the bank angle sensor too btw. Double check before you do it, but I believe if you ground out the green wire from the module it will run without it. Would be a decent way to do some diagnostic testing in the event you want to replace it. Myself, I would just get rid of it.

 

Attached you will find the wiring diagram for a 2001 sportster the 1999 should be really close. Was it backfiring through the exhaust or the carb? Personally I would look at how strong the spark really is. A weak spark could look good in the air but under compression it just isn't enough. So check the coil.