A couple of months ago I bought a 1993 gs500e from a friend who bought it off Craig's list running on one cylinder.  After a few months he decided he didn't have time or the know-how for it and sold it to me!

When I first got the bike we checked for a spark and we had one!  So we immediately started running diagnostics on the carb.  After extensive cleaning with no success I checked for the spark again and it was week.  Within a minute there was none.  Later we had a spark again and you could hear the second cylinder trying to join in but would only fire once or twice every ten seconds or so.  Then nothing. 

The motorcycle starts and runs on one cylinder but also does not seem to charge the battery.  This led me to believe that the Rectifier was bad, so I bought a used rectifier on ebey and put it on today with no luck.  The bike seemed to have even more difficulty getting started and ran briefly on one cylinder.  With the new rectifier I was getting a week spark from both cylinders but blew two "20" fuses while testing it!  I'm not sure if the fuses were related to the issues I've been having, but my electrical knowledge is very limited and I was wondering if anyone could help me!  I just ordered a used CDI in hopes that may change my luck, but if anyone has any input please let me know!  I would love to have this bike running before spring. 

Do you have a multi meter? You can check if your regulator is working properly very easily. This does not sound like a regulator problem. Sounds like you have a short in your wiring harness somewhere. Make sure you look for any naked wires and fix em up if you find some. If anything I would think the coils are bad, you could replace them both, or just the one cylinder that is not firing. The reason your spark could be weak is probably a short/bad coil. Good luck! I would highly recomend getting a multi meter though. We can explain how to use it on here.

your bike runs off of the battery and the alternator recharges said battery. either you battery is crap and will not take a charge. or you have some corroded connections for your regulator/rectifier etc. take off the side /tail fairings and you will find a bunch of disconnects. check them for greenish/white powder in them. if you do find this make sure the battery vent is correctly/completely installed to the battery. ask me how i know

Hey!  Thanks for your quick responses!  I swapped the coils and the same cylinder is still the only one running... so Im' assuming that was a pretty good sign that both of the coils should be good.  I've looked through the wiring harness and followed every cable I could checking for any exposed wires but didn't come across any.  I've considered replacing the wiring harness entirely but that would be somewhat expensive and I'm not sure it would solve the issue.  i have not checked for white/green powder but I will!  The battery was replaced a few months ago when my friend bought the bike so I'm thinking the battery probably isn't the problem. 

I have a friend who diod (sp?) tested the old rectifier and it was bad...  so I know that was one of my issues.  I was hoping putting a new one on today would solve all my problems, but it didn't.  From what I understand he was telling me that it was possible the rectifier surged the CDI and may have messed it up too, so that was the next thing i was going to replace, but I don't understand it enough to know if a CDI would cause a week spark.
 

sorry but not totally familiar with your year bike. but which 20 amp fuse blew twice. might point you in the correct direction.do you have a manual?

hey i missed one thing on you previous post, your friend said the rectifier was bad. if so it may have caused you battery to be fried. your rectifier changes alternating current( think of house power,switching from positive to negative) to pretty much straight direct current.aka what you battery is. if you get the bike running again put a meter on the battery. it should show somewhere around12 volts at idle and go up to 14 or so when revved up. if not you are not charging the battery.
the cdi unit is just an electronic switch to fire your coils in relation to crankshaft position.