NG engine exhaust manifold/downpipe trouble

[radek at istar.ca]

Hi Guys;

When removing the engine from my son's 1988 90Q for a clutch change, I  
attempted to separate the exhaust manifold from the downpipe using an  
impact wrench.  The result is one pulled-out stud (the nut wouldn't  
budge) and another mangled nut.  These things are rusted in place  
solid, like welded.  I didn't touch the two remaining nuts and got the  
engine out with the downpipe in place, lowering the subframe.

Now I'm facing a choice:  do I remove the two remaining nuts (or pull  
out the studs) and replace everything properly (four new studs, nuts  
and a gasket), or should I just fix the two problem spots?  If the  
latter, how to put in the new stud and make sure it doesn't come out  
the next time?  Red Lock-tite?  That should make the bond permanent  
but will it withstand the heat?

I will appreciate any suggestions on how to handle the  
manifold/downpipe problem, as well as what else to attend to, while  
the engine is out.  For example, is it worth replacing transmission  
mounts?

For new, the list includes new clutch, release bearing, guide, pilot  
bearing and master/slave cylinders, and new engine mounts.
Thanks.

Radek.