I recently had my clutch replaced and a new battery put in. Within a month my regulator/rectifier burnt out of it. So, I purchased a new one. After 2 weeks that one burned out also. I replaced the stator, the battery again, and the wiring harness. Now, this is my 3 regulator/rectifier that had burnt out on me. After the second one, I was told to have it mounted outside of the frame. That only lasted a week and it had burnt out again. Everything I purchased was brand new, so I was wondering if someone could help me find out the problem.
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Not Necessarily an Issue
There is not a guarantee that there is a problem with your charging system if the rectifier on your 1999 Suzuki GSXR keeps burning out.
Your era of Suzuki is unfortunately notorious for burned out rectifiers and stators. Whomever they were sourcing them through had a huge quality control issue. The TLR and TLS of that era had the same issue as did many other models. Essentially, the charging systems were junk.
Testing Your Stator
There are three yellow wires that come from your stator. They come out of the left side crankshaft cover and route into your sprocket cover and out along the cast bottom portion of your frame on their way to your rectifier. They connect directly to the rectifier. You can disconnect them from the rectifier and test them with a multimeter. Your first test will be static. The engine is not running. Be sure to disconnect from the rectifier and not just try and pierce the wires with the multimeter end. They are special wires and insulated a bit more, these are one of the few wires on the motorcycle that carry AC current.
Testing Your Rectifier
Your rectifier has diodes in it. Diodes are one way valves for electricity, think of a reed valve in a two stroke in-take. Since this is a three-phase charging system you need diodes to join the AC current into a single output and convert to DC. I could get more detailed but I want to keep it simple.
If you have lower resistance in both directions (5+ ohms) then it's shot. If you have infinite in both directions, then it's shot.
Do not buy a Suzuki rectifier. I have purchased my replacement rectifiers off Ebay fro the last six or seven years and haven't had an issue with any of them. I've purchased them all from domestic suppliers that make them for a plethora of motorcycles, ATV's and dirtbikes. You will find them by searching. I have only purchased domestic. These rectifiers have not given me a bit of issue. I have one on my son's track bike (2005 GSXR 600) since 2008 and that thing get's beat hard in the summer from 7000 RPM to redline over and over all day. The cost is about 20% cheaper than OEM from Suzuki.
[answer in progress]
One of the reasons regulators burn out is overheating. That is why people put it outside the frame on some bikes to get better airflow around them, and out of the cooker. However, given that you had done that, it must be other reason. I would suspect connections, but then again, you had replaced the harness (seems a bit rash, replacing major parts willy-nilly).
But here is something about regulator ground (via fireblades.org):