The only major difference that I've seen between the various kinds that'll work for us(91-99) is a vacuum fitting at the base of the TB.
Some of them have an air nipple - like this one:
And some of them don't - like this one:
I don't think it matters which one you get. That side ends up on the bottom in our engine bay - a very inaccessable place. If you get the one with the vacuum fitting I suppose you could use it for a vacuum source if you wanted - but you can also just plug the fitting if you didn't want to use it for anything. So either way, both styles of TB will work equally well.
As far as the intake coupler fitting...I have a short ram intake with one of those silicone couplers to fit to the TB. It is a tight fit for the Jeeper, but it works just fine.