John,
I'm slowly working through a lot of the same stuff on my '90 GL.  The big
problem with your plan as it stands is cost -- if you're going to have
someone do this stuff, it's going to be pricey.  A well-done new paint job
alone will run in the thousands of dollars; the rebuilt tranny will cost
about a grand; god only knows about the TIICO.  Just for reference, I'm
planning on swapping my 2.1 with a Boston Bob rebuild -- buy it yourself and
it's ~$2300.  I called my mechanic (who has done superb work on my bus and
whose prices aren't insane), and he said he does engine swaps for around
$5000 parts and labor.
Not sure if order of operations matters in your plan so long as you group
mechanical stuff together (i.e. plan on doing the tranny while you've got the
engine out) and the cosmetic stuff together.
Be sure to post a link to some pictures so we can see the fruits of your
labor!

Best,
d.