Update,
I decided to ditch the FI on the bike and I am taking it to a shop tomorrow and they are going to convert it to carb
... that should fix all the issues....lol
I took the bike to the Harley Dealership and they said they couldnt get the bike to misfire. But they did say my charging system was reading 1 volt low 13.5v instead of 14.5v @ 3k rpm. I was like oh well, it must be fuel related and told them to stop diagnosing it. I pick the bike up after paying $180 for their time. They were locking the doors as I was about to leave and guess what? As soon as I start the bike I it was missing and backfiring... I was like WTF? how did they not notice this? Then as I was leaving the bike was stumbling all over itself. It was missing and backfiring all the way home. So I thought about it and figured maybe the battery is just getting drawn down because they did say the bike wasnt charging at the rate that it should. I got home and was almost immediately positive that that wasnt the issue though. The battery read 12.7v with the bike off. Charging is fine, but I threw my charger on there for 2 hours just in case. Start it up to ride it, and its even worse. I had to restart the bike probably 4 times to keep it running. It would try to die even blipping the throttle. I take it for a spin. Taking off, it was stumbling worse than before and it was running even rougher. So it is just progressively getting worse. On the ride back to the house the check engine lamp came on. It was 85 degrees out and I was cruising about 55mph, so I knew it wasnt overheating. Then before I knew it the bike went to running on only one cylinder. But when I would open the throttle up a bit more, it would start firing on both cylinders, but it was still missing/breaking up pretty bad. I checked the codes as soon as I got back, it flashed codes 13, 23, and 32. It was flashing codes 23 and 32 before(even right after I disconnected the battery and I think it should have cleared any codes). The only new code was 13 for the O2 sensor. So it boils down to injector issue, fuel pump is going bad, ECM is bad, O2 sensor is bad(doubtful since it is brand new), or possibly a vacuum leak(I doubt it because even thought the problem progressively worsened, it got bad fast). Its just weird how something can go from running perfect to barely running at all so quickly, but at the same time it not being instantaneous like a part failure. Which leads me to believe its not ECM failure. Who knows, but I hope its just fuel related because if I spend all this money swapping it to carb, Im going to be ticked it turns out to be something else....lol. Wish me luck guys.
FYI, these problems arent the only reason Im swapping to carb... from what I have read, the FI system on the X1 is terrible, causes nothing but problems, and hinders your ability to make it go faster....lol. I plan to build the motor up and after speaking with NHRS and a local HD engine builder they both said that the carb is pretty much the only way to go if I want to make any decent power. So I figured Id kill 2 birds with one stone, get the bike running well and open up the doors for more power. I just wish the bike was running well so I could ride it until the parts came in