Yep, I would be really tempted to just pull it and do the engine work on the stand. Especially since you need to do the clutch too. You may also want to take one of the spare flywheels I have and get it resurfaced while you're at it. That way you can do a first class job on the clutch rebuild. You could also replace the main bearings at the same time and do the rear main seal much easier if you do it that way.
Plus, since it would take a few days to get it all done, you may be able to get someone to split the tranny/TC case apart and help you replace that seal too while you're at it.
I have a feeling that letting the parts get mis-labeled this time won't be an issue