Trying to diagnose and fix a problem with '98 R1100R

[HankPfister]

1998 R1100R with 60,000 miles (I've owned for about 7000 miles. This weird issue began on a road trip in April. It began as a sudden onset rough acceleration from a stop where ignition was cut off, then restarted. It does not occur when engine is cold and I start off, but if I stop for gas later after engine hot, when I restart the bike seems to run on one cylinder with the other kicking in as I apply more throttle. Then at about 3000 or so rpm both cylinders are running together as normal. Problem won't occur if I stop and don't shut off engine, like at a light, only after engine shut off for a few minutes. (I posted about this on Facebook MOA and got some good responses, but none of the suggestions have fixed the problem.

What I've done so far in order performed:
Fuel treatments in multiple tanks of gas (first assumption was water in gas)
New in tank fuel filter, fuel pump, and fuel lines.
New spark plugs, and wires.
New coil
New Hall Effects Sensor

So where do I go from here?

Thanks for any ideas.

 

[ksdcr]

Your description of the symptoms, seems to point to fuel starvation on the one cylinder. However, looking over your list of repair/replacement of parts, it appears you’ve covered most fueling issues.

 

[pauls1150]

The temperature clue plus an improvement at higher rpm makes me think the valves are too tight.
Another possibility could be the block's temperature sensor being at fault.
Have you pulled the Big Brass Screws to see if there is crapatation buildup on their tips or in that little hole?
(If you get new BBSs, possibly due to cracked O-rings, take an old one with you to the dealer - there are two sizes; later models got a larger O.D. screw.)