Sounds like your alternator is intermittently failing to charge the battery. You might want to check that both ends of the B+ cable from alternator to battery are clean, free of contamination, and making good electrical contact.
With any luck, someone with an '05-'06 GT who's performed the '07-'10 cooling system conversion might have one asa spare.
Otherwise search the junkyards, eBay, or Craigslist.
The inside of the throttle body between the blades and the bores may have enough dirt deposits to restrict airflow when the throttle is closed. Remove the TB and clean it thoroughly.
IMO swapping cams on a boosted set up is a huge waste of money. You could gain that extra 20-25hp by simply swapping on a smaller supercharger pulley to add 1-2lb more boost, and contact Lito to get a better tune. His email is [email protected]
Assume that weird electrical gremlins in an S197 are caused by corrosion of the terminals inside the SJB due to water intrusion until proven otherwise.
The 3V heads should bolt straight on. Although the cast iron block will add ~60lb more weight at the front, it's a good choice if you're planning to add forced induction.
Evidently the mechanics are clueless and just threw parts at the problem hoping they'd fix it.
The rattling upon start up could be a loose timing chain (failed tensioner, broken guide), and it's possible that chain has jumped a tooth or two causing the poor running.
If a valve spring retainer...