I finally took my 1997 R1100RS out for a test ride today, after getting everything back together. I can't believe I didn't have extra bolts left over after what I went through. The bike has 60K miles, and if you visit this forum often, you've probably seen several of my questions posted in the last few weeks. Here's a list of what I did.
1. Lubed all splines, including engine output with Honda Moly 60. All splines were perfect and look to have been lubed by previous owners. This job was bad, but not quite as bad as I anticipated. Clutch still had 50% left, so I left it alone. All bearings were also greased after inspection. Everything looked good.
2. Replaced hall sensor unit and alternator belt.
3. Installed new oxygen sensor and AF-XIED unit set to 7.
4. GS intake tubes.
5. Speglier SS brake lines front and back, DOT 4 system flush.
6. All new control cables; throttle, clutch, choke. Greased throttle bar and cable divider under seat.
7. New fuel filter and all new fuel lines, including in tank.
8. Converted instrument, brake, and running light to LED. Headlight converted to HID.
9. Standard maintenance items like all new fluids, spark plugs, spark wires, battery, and air/oil filters.
Finally after all these adjustments, I checked the valves and then synced the throttle bodies.
The test drive was absolutely fantastic. The combination of the GS tubes and the XIED unit seems to have increased power between 1K-3K RPM by 50%. It feels like a completely different bike. Available power around town went from good to ridiculous. Also, there is no more inflection point around 3500 where the power kicked in before. Now the power band seems quite a bit more smooth with no surging. Note; I'm not a very high revver.
I know I changed two fundamental performance attributes at the same time, so I can't really tell which one made a greater difference. However, their combination has fundamentally changed the bike's performance. If there is anyone on the fence about either change, I can highly recommend either one.
My other surprise was how easy the bike was to work on. Once the body work and tank are off, everything was accessible and easy. In fact, I'd say accessibility was superior to my R100RS. The paralever in particular was quite easily understood and worked on.
Overall I'm impressed with the bike. Now it's time to ride!
Thanks to all here who helped with my various issues.