I wish you the very best of luck on this one and please do follow up if/when you find the cure. Don't buy the next $49 piece. I own 2 of them as well as the full data/video connector now. The answer likely isn't there.
You've described exactly our problem. At ~2,500 rpm you'll see the graph of the signal flip. It probably works fine at idle right? And it probably lags behind throttle a bit when you ease upward from idle until ~3k. Above that the tach will go negative. The shift lights will work if you set the threshold down below that 3k window, so you can confirm they will work, just not at higher revs.
I'm the guy behind a few of the support question threads on TM, trying to get TraqDash to work for the '95 ITA Miata. Our only departure from your set up is that we use a Mega-Squirt on that car. When I say we've tried everything, I'm not exaggerating.
After chasing it for weeks, I felt like we were giving up when we asked Tom's gurus at OPM to take a look. They see many TMs in their cars. They, too, tried everything, including swapping known good components, tapping all the same other areas to pull signal that we did They had no luck, either. TM was consulted. My equipment has been tested and checks out...
(And that's no knock on OPM b/c we know they are good - it just validated that we weren't missing something obvious on our own).
I've all but worn out two of the TM plugs' micro-switches during the Coil to E and back testing every possible configuration and wire tap...I now own every conceivable piece of the TM solution and still can't get tach/shift lights.
The MS guys shared they've experienced the 94/95 to be a PITA where wiring and signals are concerned sometimes. In addition to the ECU swap in mid-production Mazda apparently made several wiring harness changes during 94/95, some not widely publicized. (I'll defer to the experts on that one - just repeating what was shared during troubleshooting).
My next step is to take the car and everything for Glen and the TM crew to lend their hands-on insight.
Good luck and please do report back.