I haven't done the manifold gasket, as I don't yet have the need to. But I suspect the thermostat housing needs to be removed in order to do this. Someone can verify for you. If that were the case, and this is just what I would do, I would consider doing any cooking system related work needed, even a coolant flush.
I Had everything off down to the manifold this summer. The only reason I didn't go further was because it looked to me like I had to remove the t-stat housing, and I wasn't ready to do all that when I had a coolant flush to do on my ZJ and my Discovery II at the same time. Too much all at once.