Shouldn't have to shorten the propshaft to use a J-Type. The mounting flange for the driveshaft should be in the same location. The OD replaces the tailhousing of the non-OD transmission. The OD and non-OD transmissions did use different mainshafts and getting all the parts to convert a non-OD transmission into an OD transmission can be time consuming and troublesome. The best and easiest bet is to buy an OD transmission complete. Are you sure the rear mount would even need to be changed? The mounts are the same in the TR6 in OD vs non-OD cars (they change between A-Type and J-Type OD's).
The advantage to a J-Type, other than keeping it closer to stock or at least a stock option, is that you can use overdrive in 3rd as well as 4th gear giving a 6-speed gearbox. The downside is that if the relay fails, which isn't uncommon, no more overdrive until it's replaced. Worse, if the overdrive is still engaged and you reverse the car, it will blow the overdrive clutches and it will need to be pulled and rebuilt. Luckily, there are options available out there to automatically disengage the overdrive whenever the transmission comes out of a gear into neutral so it can't be accidently left in overdrive.