You can try cleaning your MAF sensor but it sounds like a clutch or transmission problem.

 

Yeah I've already replaced it as the car was running a little rough at idle.

 

My guess is the clutch is toast and needs replacing, but is there anything else worth checking before I go down this route?

I agree with your assessment and I would also take a look at the clutch stroke sensor (check for SMT fluid on the sensor) and fluid level in the HPU reservoir. You might also have oil leaking on the clutch.

 

Pull the input speed sensor on the bottom of the transmission and check it to see if there's metal or wearing. Wearing could mean main transmission bearing going out or you hit something with it and pushed the sensor into the transmission and now it doesn't work. Metal could be nothing, just general wear from the age of the car and the sensor is magnetic and picks up everything floating in the gear oil but the sensor won't work if it gets too much. It's supposed to look like a nipple if it's good, if the center metal is flush with the plastic, there's wearing. Other than that, only things that wouldn't allow speed matching is the crank speed sensor, but there'd be more problems than that, and the speedos, but you would have an ABS warning also if one of those were bad. A bent clutch fork would also make the position sensors read wrong, but you can check that. You're going to need a true relearn after a clutch change, so if you don't have techstream, expect to haul it to Mr. T. and have them do it, shouldn't be more than a computer diagnostic.

So steps with techstream: Run it with the comp hooked up and when it does it, see what's out of values and work with that.
Without techstream: Drain gear oil, check input speed sensor, change clutch and fork, take it to toyota for relearn, if it still happens then buy techstream and adapter cord, then check values.

 

Thanks for the advice. Will let you know how it turns out.