Rather than type everythign out and start from the begining here's a link to where i posted this on the 900RR forum.



https://cbrforum.com/m_137502/tm.htm

 

Checked the link, had a look at wot the others had to say, seems like that had it covered. My opinion, for wot it's worth, (you may have started out with a common garden variety short), but you have to have your regulator checked to eliminate that from the equation that this is your main problem. From wot your describe, it's exactly how a reg goes, you only get a couple of warnings, (like the battery going flat).
If after you have it checked & it's not the reg, then it's time to go through the fault finding exercise.
Either way your going to need someone with the right tools & expertise to track it down.

 

I also have a 93 900 and had the same problem. I was flyin down the highway to work in rush hour traffic and all of a sudden the bike bogged out like I ran out of gas and stalled on me. Got it to the shop and the rectifier went out and burnt out the connector and was so hot made the connector to the fuel pump expand and come undone. Replaced the rectifier and two weeks later bike did same thing, this time I had to replace the stator. From what I read they kinda go hand in hand sometimes. hope you get it all worked out. Good luck!