I have a ’95 CBR900 but the charging systems are similar.

1 OEM RR unit fail (not charging the battery) replaced it with an aftermarket RR unit of similar design which also failed (an unregulated 17+ VDC killing the battery) so, reasoning that heat build-up was at least part of the problem perhaps exacerbated by the quality of components in the RR, I replaced with an aftermarket externally mounted aluminium finned unit which has been good for the last 75,000 kilometres (46,000m).

Also the multi-connector for the 3 phase from the alternator to the RR cooked during normal operations i.e. since stator output was ok (about 75 AC@5000 rpm), the original equipment was not up to the job, not an uncommon problem, so I replaced this with individual insulated crimp connections and have had no problems since.

A check on EBay shows lots of stators and RR for CBR for sale, an indication that these items fail, though I have never had a problem with stator output.
The manual for your bike has guides.

There are .pdf flow charts on the interweb to download for RR diode checks.
http://www.electrosport.com/technica...ting-guide.pdf

Here is a link to stator checking with photos
http://gsarchive.bwringer.com/storag...ator_check.pdf

also good link for stator checking
HOW TO: Test and Replace your Stator - Important/Useful Threads - CBR1100XX.org Forum

So, perhaps follow the checks from stator winding ohms, to stator output to the RR to DC from the RR to the battery (13.5 to 15.5 @ about 5000rpm) and looking for any signs of bad connections/heat stress.

 

Update: Purchased new R/R from Rick's Motorsports. I have checked the charging system periodically over the past 300 miles and everything continues to work as it should. I relocated to the new unit to a cooler/exposed spot on the bike and haven't had a problem since. Fingers crossed...Thanks all for your input while trying to to chase down this issue.