I have a 99 gt with a lightly moded motor.  mods include CAI, P&P TB/plenum, diablo tune, tri ax shifter, underdrive pully kit, off road x-pipe w/ side exit glass packs, subframe connectors, jacking rails, matrix braces, lowering springs, strut twer brace.  My question is what gears should I use.  I was going to get 373 but heard that I could go higher.  some people tell me to go with 410s while others say 410s are to high.  A 390 is available which I thought I might use, but now Im not sure.  any help would be greatful.  Thanks  

a 373 is a good all around gear both streetable and raceable  

The important thing to think about is what you are going to use it for.  Is this around town daily driver, highway commute or travel or a weekend use drag racer.  If you are going daily driver I would go 3.73.  Weekend drag car I would do 4.10.  Besides that MMFF likes to say that "it is only a couple RPM so it doesn't make a difference"  It does especially if you have loud exhaust at highway speeds the droan can get irritating.