I've got an 08 mazda 3 2.0l 5 speed manual. I also have a 2006 mazda 3 2.0l 5 speed manual. I bought the 08 knowing that 3rd gear was out and I had the 06 as a parts car. I was driving the 08 until it lost 4th gear as well. So I pulled the trans out of the 06 to put into the 08. Since then I have had issues. The trans works just like it should but my alternator goes from not charging and my battery draining to it over charging charging. I have pulled the alternators out of both cars and had them tested and they both were right at 14.5 volts. But in the car they both sit around 16 volts. I've replaced the battery a couple times. I even replaced the pcm since the voltage regulator is in the pcm. I've tried to take the sensors out of the 08 trans and put them in the 06 trans which is now in the car. When it's not charging the car will stutter when driving but it'll keep running all day so it's gotta be charging a little. The headlights flash on and off unless you have the headlight switch on and then they have no problems staying on they only flash ok and off if the switch is turned off. The interior lights come on and off as well as the gauge backlights. I've tried to swap just about everything I can think of and nothing changes. I've checked grounds I've checked fuses I've checked wiring all are fine. Code reader won't pull codes unless the car is off and left off cor a couple minuets. Trans works great. Someone explain to me why everything is fine but when I change a manual trans, that has nothing to do with the computer, why do I have all these issues now and how do I fix it. I've tried everything including ripping my hair out.

 

2007 Mazda 3, similar issue. Family friends car, I noticed low beams out. Changed bulbs, they failed by next day. Found battery charging as high as 16.4, very jumpy. Figured failed VR on alternator, test at Autozone showed not regulating. When car was running and voltage went particularly high, the low beams flah and dash lights dance.
Changed alternator, same issue. Brought alternator back (failed new part, no shocker), tested ok in shop. Tested at another shop, tested ok. Reinstalled alternator, swapped out battery, no change. Very erratic at times, averages about 15.5vdc charging, low as 14.2 to16.3. Used OBDII watching live, voltage reading approx 1.5 - 2vdc less than measured at battery. Have tried replacing grounds, cleaning ground points. If I could find an actual list of ground points, that would be useful. Using Haynes Manual as primary schematics. Took to a "Mazda specialist" who told me the 07 does not use the PCM as regulation, has to be an alternator problem. Going through electrical points now trying to find the voltage drop.
Not enough hair to keep pulling, I have shifted to banging my head on bumper of 63 Dart.

 

Was anyone able to pin point the issue with the overcharging and voltage drop?