BobE wrote:

Congratulations on Sherry's retirement and the new house.
To the new garage I'll add you to consider LED shop lights.  These are extremely bright (something I need), and area a bit expensive, but in the long run ...
Good luck

 
Totally agree with Bob on the LED lights. I replaced my (new ballast & tubes) florescent lights with LED light and the difference is amazing. I bought mine at ELEDlights.com, but I have heard that Costco carries a very good "shop light" style LED fixture.

I've always thought roller doors would be a great space saver.
  
http://www.thegaragedoorcentre.co.uk/rollershuttergaragedoors

I have the highlift garage doors that hug the ceiling. You can only do it on the single wide doors not the double wide doors. This was done to put the lift under. 
Also look at the Liftmaster Jackshaft Garage door opener. It sits on the wall and leaves the area above the door clean. 
http://weshipgaragedoorparts.com/LiftMaster-8500-Residential-Jackshaft-Garage-Door-Opener_p_12.html?gclid=CjwKEAjwutXIBRDV7-SDvdiNsUoSJACIlTqlRhja1-SojFtG0dqEgQpqXL9irPVhTIOvFx6dwFqiIBoCOnTw_wcB​

Yeah, $50/sq.ft. isn't going to get you what you're talking about.  A plain vanilla garage with vinyl siding and no real interior maybe.  When you add things like insulation befitting a house, drywall on interior walls/ceilings, real electrical, gas piping for heat, stucco exterior, etc. you're getting close to house construction costs.  At that point you basically are building a house without interior partitions and floor coverings.  $85/square foot doesn't sound bad at all.  I put in a proposal for one a week ago that was $93/ square foot and about the same level of finish, but only an 8' ceiling.  Every project is going to be different based on the layout of the lot, local requirements, and labor costs do vary considerably by region. 

One option is to consider what's easiest to put in it now, and what can be added later.  Also, what can you do yourself with the help of a few buddies and some beer.  My shop started life as a pole barn designed to house my dad's helicopter.  Literally a building to keep it out of the elements.  No insulation, no heat, minimal electric, etc.  Over the years he added insulation, heat, and changed the door configuration when he no longer needed it for his chopper.  Later I added a loft to part of it, considerable shelving, a lift, and AC.  When I redid the roof a couple years back I added a 2' overhang front and rear, and extended the side overhang to 2' and added floodlights all around.  Future plans call for siding (I'd like cement board, but might have to go with vinyl for cost) and a shed roofed storage area around back for ladders, etc.  I never could have done it all at once, but over the years it was possible.  Granted I had a much longer timetable than you will, but something to consider.