Hi Geo,
Sorry to hear you are having to remove the gearbox to resolve the clutch issues.
I've never used that bolt alignment method when removing or installing the TR4's gearbox. But, it might be useful, particularly when re-installing. On TR4, originally there is one stud at the 12 o'clock position on the bellhousing, and that's all the alignment help I've ever needed. Yes, if the clutch and pressure plate are removed or moved in any way, an alignment tool or dummy input shaft to align the splines with the pilot bushing will make your life a lot easier when you go to reinstall the gearbox.
Once the interior bits are out of your way and the starter removed... yes, the driveshaft can be completely removed, but the front section might slide far enough back on the splined joint to make that unnecessary. Depending upon exactly how the exhaust system is run, some parts of it might be removed, too, for a little easier access. This might be unnecessary, though.
Others noted lifting the rear of the engine with a jack under the sump, which shoiuld be protected by a flat, wide piece of wood on top of the jack. This is actually mandatory to remove the gearbox, since you'll need to raise the rear of the gearbox before it will slide out. For easiest access, you'll probably want to remove the nuts and bolts around the top of the bellhousing *before* lifting the rear of the engine and tilting the gearbox up. The firewall will make it difficult to get to those bolts after the engine/gearbox have been jacked up a little. Once the rear of the gearbox is loose and you are ready to lift the rear of the engine, have someone slowly jack up the engine while you are watching the throttle linkage that goes across the firewall, right behind the engine. That's what limits how high you can jack the engine. You only need to lift the engine an inch or so. Just leave the engine slightly lifted until you put the gearbox back in.
Thankfully, the TR gearbox is not terribly heavy, about 70-80 lbs empty of oil for the non-OD unit, about 120 lbs with OD.
One suggestion, assuming it's an original "thin-flange" TR4 g'box in your car: When reinstalling the gearbox I personally think it's a good idea to replace all the various nuts & split-type lockwashers with nylocks or jetnuts and plain, flat washers on the gearbox side at least. This because the thin cast aluminum flange at the bellhousing can sometimes crack and break due to stress. It's a known weak point and was beefed up on later cars. IMHO, using larger diameter plain washers here helps to spread the stress around a bit and better support the bellhousing-to-engine mounting point. With plain washers, the nuts need to be self-locking, thus the nylocks or jetnuts. BTW, I opted to replace all the original bolts with good fitting Grade 8 sized so that no threads ended up inside any of the mounting holes. Probably overkill... but what the heck! /ubbthreads/images/graemlins/smirk.gif
Hope you find the clutch problem is easily resolved, once the g'box is out.
/ubbthreads/images/graemlins/cheers.gif