Thank you guys for all your help. I got the bike running again yesterday. Not exactly sure how, but there are couple possibilities. I re tested the old ignition coil completely by itself (with a different set of spark plug wires) by plugging the positive pin 15 from the primary pin to the battery + and another wire from the pin 1 to the frame while I had one spark plug in the engine and the other plug against the frame. This time I got spark. Re plugged everything to the new ignition coil and nothing. So I replaced both wires running from ignition coil to spark plug and it worked. I did test the wires with a multi meter before and they were good. For some reason couldn't get a continuity reading on any of the 4 wires this time? Maybe one of the spark plug wires has a fault and only shows when the wire is bent?

I did have the motronic control unit out for an entire day as well so maybe it finally reset itself. Previously I only had the battery unplugged for about 30 min and it didn't make a difference. Or maybe there was a ground fault that got fixed while I removed/re installed things. I did run a separate ground previously to test the ground, but it didn't help.

What ever it is i hope it is not a fluke. Again thank you for everyone's input. I learned a great deal about BMW in the process and found several issues that needed fixing anyway. This forum is an invaluable asset for DIY guys.

Mahalo from Hawaii.

Glad the bike is running.
You can't go wrong with a new pair of ignition wires on a 1998 bike.

I am having no spark issues on 2004 R1100S twin spark.
Fuel pump cycles on
ECU power at fuse and at #30 on relay have power and fuel pump/ ECU relays have been switch showing they both work since the fuel pump cycles
Neutral light works
bike is in neutral and kill switch is on when trying for spark
Clutch position and kick stand position cycle the fuel pump as expected
Wires from to key to electrical box all pass ohm check
Fuel pump cycles on and off when spinning the engine over with the rear wheel and the key on - (shows HEL / HAL sensor is working
Used coil tired
Used ECU tried
HAL / HEL replace with used (see above testing)
bike ran and did not restart after getting fuel on a dry night