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.
[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):
The biggest problem with rectifiers, and in my experience why the burn out, is the lack of a good ground to the battery. The back of the regulator is metal and is supposed to ground against the frame. After a year or two, the aluminum gets a layer of oxidation on it that makes the gound very weak. The rectifier, which uses the ground to determine battery voltage, thinks the battery is low and over charges in an attempt to get things back to normal. This usually burns out the reg or battery or both.
Running a ground wire to one of the bolts on the reg with a big round wire end that contacts the back of the reg almost always fixes the problem. As long as the system isn't too damaged. The over heating in the system also often causes the connector plug between the reg and the stator to go bad as well, so be sure to check it for melting or bad wires.
Edit: Here is another possible issue — surges or shorts in high-voltage ignition system that can fry components of low-voltage system (see answer from Suzuki GSXR600 (K7) - Burned regulator/rectifier question).
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.
Static Test Set multimeter to ohms and test between all the leads in pairs. The reading 0.1 to 1.0 max resistance.
No Load Test Dynamic Test Set your multimeter to AC Volts and start the bike. It should be cold. Have a friend hold the RPM's at 5,000. Test between the leads. You should see more than 70V. If it's below that, you may need a new stator. I would replace, but I'll get to that later.
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.
Rectifier Resistance Test Using your multimeter set to ohms connect the multimeter to the ends of each of the diodes and check the resistance in both directions. You should have low resistance in one direction and higher in the opposite direction. Generally, you will want to see 5 - 40 ohms of resistance in the forward bias direction, and infinite resistance in the reverse bias direction.
Procedure Attach the black probe (-) of the meter to the ground side of the rectifier (black wires) and the red probe of the meter to each of the three contacts for the stator. Record the numbers. Then swap around the meter leads (red and black are swapped) and take the readings again. You have thus measured the ground side of the rectifier.
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.