Well, after getting everything put back together, I now idle at 1400 rpm. I added more fuel in the low end, but I am going to go more. Should be pretty good after that.
Sounds like you have messed with the cold/warmup idle screw, the warm/hot idle screw, or both.
When the bike is dead cold start it up and see what rpms you have. If the cold rpm is too high or low shut it off asap so unnecessary heat builds up so you can retest after adjustment.
(You may have to back off the hot idle screw because it is confounding the warm up adjustment)
Once you are happy with the cold startup idle speed, let it completely warm...like ride it around for 5 mins. Once completely warm readjust the hot idle speed to 900-1050.
Once this is done unplug the ECM fuse under the righ side cover in the cute black fuse holder for 5mins.
Plug the fuse back in and ride.
THIS ASSUMES THE IDLE - 1500 rpm FUEL MIXTURE IS CLOSE. Gotta be close enough for the mechanical idle speed control (ISC) to work properly.
If you do not have a way to measure AFR and think you will be able to guess your way through a Magneti Marelli idle setup and tune, I can tell you from many years experience working with these MM EFI systems, it will drive you completely nuts trying to figure out how get the thing running right.
There's 100s of threads in the Harley forums out there with folks trying to get it right.
Find a tuner that really knows MM EFI and you will be very happy. Otherwise find an Indy who will convert you to a carb then ride.
Hope this helps,
Bob