Oh OK, I am not familiar with the Corolla model variants.
Now that I know this car is a manual, @mathers402, I am really surprised that you replaced transmission components while the engine idle speed is fluctuating in neutral. Have you had the car scanned for codes? fluctuating idle could be caused by a few items: Off the top of my head, bad throttle body, bad idle air controller, bad VVTI controller to name a few. Get the car scanned and go from there rather than blindly throwing parts at the car. Already 45k has been spent chasing this fault with no solution so far.
It is my guess that your loss of power in 1st and 2nd gear is down to an engine fault and nothing to do with the transmission.