Congrat's, great buy!
#1) Go fast with little or no $$, if you ever discover that one, definitely share that knowledge...because usually those two don't go hand in hand. If I were you, I'd probably look into investing in some cams, either Type R or Skunk 2's.
#2) They should unbolt from the top, not too familiar with 6th gen Civic's.
#3) Front Strut bar ( a good one) & a sway bar kit would suffice.
#4) For the VTEC controller, your best bet is to tune it at a dyno.
#5) Enjoy the car, keep it secure and you will love it.