2 things come to mind:

'65 gearbox bellhousing won't accept the larger 12V flywheel which the Trekker has.

'65 throwout bearing needs a pressure plate which has the centre thrust ring.

I have some info and pics on my web site here:
http://www.speedyjim.net/htm/6v_12v.htm

More electrickery on
Speedy Jim's new web site:
http://www.SpeedyJim.net

 

The engine is mated up to the box it just needs to slide back 2 in ?

 

What happens if you turn the engine pulley by hand whilst pushing the engine in?

 

The engine is fully in?

 

No.
With the 2" gap, push on the engine AND turn the pulley.
If you hear the flywheel teeth grinding on the bellhousing then it ain't gonna go in.

 

If I take out cylinder covers will I be able to fit them in when engine is in?

 

Valve/rocker cover?

Yes, it will still be a tight fit but can be done.

 

Cylinder head tins

 

Dunno. Looks tricky.

Anyone else??

 

Fitting Cylinder head tins with engine in-situ, should be possible if the fan housing and manifold have been removed. Will probably need an assistant to help line-up the bottom tins at the same time.