Jeff,
I just went through all of this by adding on to my existing three car garage. Like you, my property size and shape dictated what I could build, so your idea of building a model to think about how you will be using it is a good one. I didn't go as far as building a model (though I should have), a drawing to the same scale as Hot Wheel cars really helped as I tried different layouts, what would have to be done to move cars around to get them in and out, etc. In addition to my existing four post lift, I added an inground scissor lift near the garage door, which allows me to work on daily drivers, cars I'm detailing, etc without moving the inoperable cars in the back. The garage at out previous house had a 10' ceiling, and I could not go all the way up with a '66 convertible on my four post. An extra foot of clearance above the lift will make a big difference.
As others have mentioned, LED lighting is the way to go now. Based on the big lighting threads at the Garage Journal, I shot for 100fc at 3' off the floor and used one of the recommended vendors for the lights. I ended going with a bunch of new 4' fixtures (~$14 each) and two 2650 lumen 18 watt lamps (~$7.50 each), so about $30.00 for per fixture for over 5000 lumens. This was early this year, so you can probably do better now as the technology continues to get cheaper.
A few other thoughts of the top of my head:
I split the existing three car in the center so that one side is climate controlled and where I installed a urinal, which has been VERY nice to have, as well as a deep commercial style sink.
My compressor is in a separate room that I use for storage, but outside would be better, particularly when I'm blasting for hours at a time and the storage room gets really hot.
Lot's of options for flooring that get debated, but I went with epoxy this time and really like how easy it is to keep it clean, wipe up spills, etc. Had a Racedeck clone at my old house, and anything that was spilled went right through the joints in the tile and into the concrete below.
Every window and door is lost space for storage, etc, plus another way for someone to get in, so I believe in minimizing those as much as possible while trying to match the styling of the existing house.
You can't have too many electric receptacles. I put a bunch of them on the walls, both at 16" and 52", but now wish that I would have put more than the two I did on the ceiling.
If your lift is going to be near a garage door, you will want to consider a 'high-lift' style track for clearance.