I have been looking at the same thing recently and you probably found plenty of info. If money is no object then look at a Trick Flow street type top end kit at late model or Jegs. The best early results are heads, underdrive pulleys, air box silencer removal. Items like exhaust, throttle body, cold air filter work better after heads. Exhaust sounds like more HP and gears feel like it.
I heard The official Ford 5.0 technical reference and performance handbook is good but its $50.
I'm still thinking since mine is low miles and still stock as 88, maybe I'll find something else to have fun with but still checking Craigslist for aluminum GT40 heads. Check out the 88' vert on bringatrailer.com from March 9th, untouched Fox stangs are becoming rare.
This link is helpful since these guys had a dyno: 5.0 boltons dyno results [Archive] - DFWstangs Forums