Don't forget the cost of a properly set-up QT tank as well eh?
Go talk to Mike, Jeff, or Jack at J&L Aquatics. They'll set you up proper.
90 or 120 would be roughly the same cost. Not much difference. Maybe a few hundred...
As far as the main equipment for a REEF, I would buy:
~ Euro-Reef RS-180 skimmer (don't like the 135 for various reasons, and the 100 would be too small)
~ 2 x PFO 250W HQI Mini MH Pendants w/ Giesemann 13,000K bulbs
~ PFO Dual 250W HQI ballast
~ PFO Dual 48" VHO retrofit kit w/ URI Super Actinic bulbs
This total would be about $1700 from J&L including bulbs and tax. About $700 for Tonga live rock and sand. If you buy an entire setup and talk real nice they'll prob give you a deal. So that leaves you with about $600 for a tank and QT to choose from, which won't be enough. I wouldn't consider any other equipment, haha! Might want to consider buying a used tank...preferably one with all the plumbing. You'll also spend another $3-400 on return pumps, and about $50-100 on plumbing depending what you want to do. I think $3000 isn't enough for a tank this size...you need $4000 to do it comfortably. Maybe try a 75 gallon? Or just buy an entire set up used...? More fun to build it I know!!!
You could just go all VHO lighting and do FOWLR. You could do that for $3000.