In the future, PB Blaster will become your best friend. Rust penetrating spray you can get at local auto stores or Walmart. That plus alittle heat from a propane torch does wonders. Last resort is a grinding wheel or cutoff saw.
Those were probaly the hardest bolts to do in the whole job. Working on any exhaust bolts in a rust belt area of the country sucks. Those are the bolts that you should replace.
Just keep plugging away at the smaller jobs and you'll soon be doing your own motor/tranny swaps!