Motorcycle Repair: 98 Ultra Evo runs poorly when hot, oil seepage, hd factory

Question
'98 FLTCHUI 43,000 miles with Stage One and ECM w/proper download.  Bike has been babied all its life, never redlined, rarely over 4k rpm, and oil changed always 3,000 miles or less.  Starts fine and runs beautifully when cold and does not show EFI warning or flashing lamps.  With engine thoroughly warmed up, after riding at highway speed for awhile at about 3,000 rpm or so and then letting rpms throttle down (like slowing for traffic or exiting freeway) engine goes bleaaaah when reapplying throttle; feels almost like engine floods, as if you were on a carbureted bike and pulled the choke full out and tried to accelerate.  It's not a miss-- just a full out lag.  Also, when this happens I sometimes smell some unburnt fuel.  IF I baby the throttle and bump it back up slowly, it will purr along at highway speed until the next time I back down the throttle...sometimes! Sometimes it doesn't happen for 30 or 40 miles and then starts again. This intermittent problem does seem to be getting worse and happening more often.  Lately, on occasion it feels as if it would stall when backing all the way down to idle, but if I baby the throttle back to about 2k rpm, hold it there for a bit then slowly back off it eventually seems to idle ok.  Local HD dealer shop replaced intake gaskets, ran diagnostics on EFI sensors, tested fuel pump on Dyna, checked fuel injectors, found nothing. They then ran a compression/leakdown  test and found 10% loss on front cylinder and 15% loss on rear. Also noted small cylinder base gasket oil seepage/leak; more on front than back jug.  They say I need a full top end rebuild or a HD factory remanufactured engine.  Does that sound right to you?   Many thanks.

Answer
You might need a top end done, but that is not what is causing the problem. Lower compression and your leak will not cause your problem. At 43,000 miles you surely dont need a remanufactured motor!
It sounds like either your EMC or the pickup is starting to go out. When they test it, it might be working fine. I would have it run on a Dyno and make it do the problem and then see what is happening with the EMC
Good luck and happy riding
Mike