[D13]

If TBI, why not just bolt on the GM unit? $150 in the j yard, including the throttle body (not included in $600 megasquirt), ECM and wiring. It'll adjust for altitude, it has closed loop feedback for changes in fuel (warning - it does not like over 10% ethanol). Just need to redo the 4 center manifold holes and you're good to go. Fuel plumbing will be the same with either system. If you get a complete donor harness with the 700R4 connectors you'll be all ready for that swap, can get a chip burned to ignore the trans in the mean time. Don't know about your area but around here you can buy a complete running 350 TBI 700R4 88-92 1/2 ton for under $1000. Could do the complete swap and then your 350 would be available for the rebuild, or you could rebuild the roller cam bock.
TBi will give a little better MPG (like, maybe 1). A lot better cold start and cold driveability, will adjust for altitude, and bette fuel control leads to great engine longevity.

if you go megasquirt might as well step up to port fuel. Where MS really shines is oddball (think dual TBI on an inline, or E85 port fuel on a 300 ferd). For basic 350 TBI it's hard to be the GM units.