The reason it's not recommended that you remove (and or replace) the box leaving the TC attached to the driveplate is that there are seals on the main shaft that can be damaged - obviously fluid flows and returns to the TC via passageways in the main shaft assembly. The seal on the gearbox front cover only prevents fluid leaking from the box.
If those seals get damaged you'll end up with little or no pressure and the box won't operate. They usually need the box to be stripped to replace.
I think you may have found your own problem.
When removing the engine it is vital that the TC stays as far in the gearbox as possible, unbolting it before undoing the bell housing bolts and preferably holding it in the gearbox (during and after engine removal) with a physical restraint. (bent bit of metal, cable ties, whatever you can)
The clang noise you describe was probably just the ring gear catching something and releasing making the flexplate ring like a bell.
This seems to be closest to the likely problem, and thanks.
What I've now done is pull the engine out again. With the torque converter off there are three concentric shafts with splines on. The two inner ones just rotated freely, but I've now manipulated the middle one, that is the one in between the centre shaft and the outer so it sits further back and is engaged on something.
The very centre shaft still rotates freely though and doesn't seem to be attached to anything. at the inner end. Can anybody tell me if this is correct?
I think you will have to suck it and see, without finding someone local that has actually done the same thing on that set up who could take a look, it is just down to fit it all back and cross your fingers.
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