That was one of the first jobs when it followed me home as a basket case, before installing the wiring harnesses. It does act like a bad ground or flaky connection though with how it just "switches" from behave to dung-heap mode, so will take your advice into account and go after the grounds first off (if only to re-confirm good continuity).

One thing I've noticed is, when it's acting up now it's not doing the rich/lean thing just purely dropping lean & if I hold the start button down for start enrichment it actually seems to run fine then.

Also, last night I checked the TPS as it appeared to make no difference & it's not acting quite right. IIRC it's just a pair of switches right? One closed at zero throttle and the other closed at WOT?  Can't find the pinout/test on Drake's site that I recall previously using, but either way it now seems to have flaky "closed" resistance & "open" there's 25meg or so between all pins. Sounds wrong to me so will try and search out the testing for that again & try some diagnostic bodges if it won't clean up.

Cheers 

One of these small motorcycle stands is kinda nice to have around for working on these bikes, and its compact so it stores easily, and its a bit easier to use than blocks.  It will hold the bike up from the oil pan(remove any engine spoiler and be careful of your headers) no problem and its pretty stable like that.  It's what i use when I cant use my center stand(like for gearbox work).  You can usually pick them up for around $50(US) and they take up no space at all when not in use.

Although you might not yet have completely recovered from Rifa madness, have you cleaned the main ground connection beneath the frame backbone and all terminals attached to it?

The grub screw was the first job I ever did on a Brick.  Took about 8 hours start to finish and didn't require any special tools.  Just take your time.

The transmission splits fairly easily and is just a little fiddly to get the cases back together, but not real bad.  As I recall, the worst part of the job was getting the grub screw back in after I cleaned it and applied blue Loctite to the threads.  I dropped it into the transmission a couple times and had to fish it out.

While you are in there, it is a great time to lube the clutch splines and replace the clutch o-ring and maybe the rear engine main seal.  Be very careful with the clutch boot or you will have to replace that too.$$$

Take your time and bag and label the stuff you pull off as you go.  This will save a lot of time when you put it all back together.  You will need a stack of blocks to put under the engine when you remove the transmission.  As you reassemble, put a little anti-seize and and torque all the fasteners.  Install new brake pads, lube the drive shaft and change the transmission and final drive fluids and the entire rear of the bike will be in top shape when you are done.

When you DO get it on the road (note I did not write IF) you will probably have taken the gawdawfulest pile of marginally useful scrap BMW and turned it into something.

Turned it into a gadawful pile of marginally useful scrap BMW that screams down the road looking full well like it just fell out of satan's ass? 

As far as the electronics goes, it's a combination of not having the liquid funds to throw at "possible" fixes & a perverted desire to fix anything/everything down to component level where vaguely practical.  The RIFA cap replacement in the ICU obviously wasn't the fix, although anecdotally/subjectively the spark seems a little hotter with them done it's more than likely placebo.

Will attempt to remember photos later on, it's still ugly as a bag of verruca-ridden feet that just walked across hot coals and dog turd though just vaguely more roadworthy-looking than it was before.

When there's time to get it done, I think it's earned an oil change and real coolant then possibly test-ride as it is & see if the hardtail idea is a goer or not. Cheers