First of all, thanks for providing a clear description of the problem, symptoms and such. Diagnosing at a distance is always difficult, so any and all relevant information is always very important.
In short, I agree with that the engine and clutch/gearbox issues are more likely than not separate issues. Some of the symptoms you descripe sound more than familiar to me.
1. The bike suddenly dying and refusing to restart, though cranking fine: one option is a failed intake side cam follower bearing. Read my experience here
(the start of that particular saga), more general documentation and discussion here
2. The clutch changing it's feel along the way may simply be either the master or slave cylinder (or the respective seals) coming to the end of their useful life, causing the leaks. A rebuild with new seals may be all that's needed here. Other option, which is actually totally separate from leaking seals but causes somewhat similar symptoms is well detailed in these two threads, here
. I recommend reading all the pages of both threads closely.
3. The leaking shafts are a known issue with the LC4 (see here
for the fix). However, if the start of these leaks coincides with only this "incident", I would be willing to wager there might be something more going on inside the engine. It is not unknown for the transmission bearings to let go, allowing the transmission shafts to wobble around excessively in the cases, causing all kinds of damage (one fairly mild example here
All in all, I think you need to do some further diagnosing. However, I envision a engine-opening excersise (case-splitting) in your near future. For that, some good reads (besides the LC4 index thread
with links to multitudes of info, you are familiar with it already, aren't you?) are these:
Gunnerbuck's 127,000km rebuild thread
ClintNZ's rebuild thread
Three times the fun! - rebuild of 3 LC4's
LC4 routine maintenance
...and many more of course, links can be found from the index thread