The only issue you may run into with the regal trans, would be the trans cooler line connections (your 99 may have screw in fittings, while the 00+ will have push clip style).
The intrique trans could have a different final drive as it is mated to a different motor. It may be the same so you would have nothing to worry about. Also the final drive is a pretty easy swap.... a few bolts and 20 minutes could get it swapped out.
Torque converters will be of no concern.... anything you get will be close enough.
