Then it's the stator/alternator?

My bike (96 F3) left me stranded at work, battery died while running. A friend gave me a ride home, he knew a guy who had a similar problem with an F3. I talked to the guy and he said a new regulator/rectifier fixed his issue. So I followed his advice and put on a GSXR unit. I charged the battery and yesterday I was riding home. Well, after about 20 minutes of riding, I noticed the RPM fluctuations that I had experienced before which were indicative of an impending failure. Sure enough, as soon as I released the throttle for the red light, it died.

So I'm guessing the stator/alternator is the problem now? Is there anything else it could be?

You could have gotten a bad RR or it could be the battery is bad now. It also could be the stator... you just don't know until you test them out. The battery you can take to some where like batteries + or something like that and they can put the battery under a load test. This will tell you if the battery good or not. The next part, you will want to follow the flow chart that I've put a link to. It take a bit of time but it'll tell you exactly what is your problem. You should also check the connections in your harness, make sure they aren't burned up.

Here is the link to the flow chart: http://www.offwidth.co.uk/bike/general/electrical_fault_finding.pdf

Another good troubleshooting: http://cbrworld.net/forums/thread/140473.aspx

The battery holds a charge fine. Checked out at 13.0V. I started the motorcycle, revved to 5000 rpm, 12.3V. When I replaced the RR, I soldered the connections directly since I used a GSXR unit. I can't find a plug with 3 yellow wires aside from the 3 yellow wires by the RR, so I suppose this is where I have to do all the stator checking? When I installed the RR, I cut both plugs and soldered the RR directly. In hindsight, I probably could have gone about things better. I'm off to home depot to pick up a few things, I'll see if I can get some connectors. I'm fairly certain the wiring job I did is good, but it's worth it to check and do a proper connection fitting before dropping a couple C-bills on a new stator.

It sounds like the stator may have been the problem all along. Those three wires coming out by the stator are the ones you want to measure the resistance one. Measure across all three leads, 1and2, 2and3, 1and3. they should all be close to .7 ohms. Follow the flow chart. If any of them are out of spec, then your stator is the issue.

Now you have to hope your wiring job isnt what blew the stator and the stator was bad all along. Triple check all of your wiring to make sure its good.