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Aligning the clutch and refitting the gearbox can be difficult particularly if the engine is still in the car and you are working from inside the car.  The gearbox is very heavy and you need to duck under the instruments and glove tray while lifting and aligning everything.  Even with the gearbox supported on a substantial trolley jack it can be quite a balancing act and nothing seems to quite line up.

There is no magic wand which will make the process easy but there are a couple of tips which can make it much easier.

Presumably you will already have removed the front seats and the front floor boards to get the gearbox out so access should not be a problem other than the physical contortions required.   It is essential that the clutch plate is accurately centred on the flywheel before the clutch cover is bolted up.  This is easiest done with a clutch aligning tool and it is but a few moments work to make one.  Get a piece of bar (an old wood and rubber valve grinding tool is ideal) and build up the diameter of one end of the bar with sticky tape until it is a good fit inside the flywheel centre bush.  Push it into the bush and the bar should now be sticking straight out from the flywheel.  Slide the clutch plate over it and hold it in place against the flywheel.  Make a mark on the bar to note where the plate splines fit over the bar.  Remove the plate and the bar and again use the sticky tape to build up the bar diameter where  the splines were until the splines are a good fit on the tape

Now slide the alignment tool inside the clutch plate splines checking that it is a tight fit and then insert the tool into the flywheel and push the clutch plate against the flywheel.  The clutch plate will now be properly centred and you can bolt up the clutch cover with confidence.  Tighten the clutch cover bolts progressively and finally check that the bar which sticks out of the cover is still properly centred in the cover.  If all is well, pull out the alignment tool and put it safely away for future use.

Ensuring that the plate is properly centred does not automatically ensure that the splines on the gearbox input shaft will line up with those in the clutch plate.  To make this happen, put the gearbox into gear (top is fine) so that as you turn the output shaft at the back of the gearbox the input shaft also turns.  Now as the clutch slides into place a small turn of the output shaft will bring the splines into alignment.

Of course there still remains the heavy work of getting the bell housing onto the studs, sliding it in at the correct angle and turning the output shaft to align the splines.  This can be made much easier by replacing two of the studs on the back of the engine with longer ones.  The ideal ones to replace are the ones at about 2 o'clock and 10 o'clock and the ideal replacement are old cylinder head studs from a 1½ litre engine.  If these are not available, use a length of studding or a long bolt with the head cut off.

Now side the bell housing onto the long studs, lift and back end of the gear box so that it is square to the flywheel, slide it forwards until the splines try to engage, turn the output shaft a little while continuing to push the gearbox forward gently.  You made need to give the back of the gearbox a little wiggle/shake before everything slides in. 

Once the bell housing is on the long studs you can safely let those studs support the front of the gearbox thus keeping your fingers out of harms way and leaving a free hand to line up the back of the gearbox. 

With the bell housing safely on the short studs, fit some of the nuts and then unscrew the long studs and replace them the original short studs.  You can now bolt up the nuts tight and refit the gearbox mounting bolts.