- 12 shop light fixtures built into the ceiling
12 fixtures is a lot. Here is my 30X40 at night with 7 fixtures. I don't foresee ever wanting more light from the ceiling, although I'll need more underneath cars, over workbenches, etc. in the future.
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You can never have too much light, though. So, if you stay with 12 - I'd definitely suggest having them split out on multiple switches. (You won't want to light the room up like the sun to go in and fish through your toolbox for a second and then go back inside.) I'd also suggest checking out the threads on this site regarding hooking the lights (or some of them) up to a relay or lighting contactor driven by your garage door openers. (So, your nice lights come on instead of a single bulb on your opener.)
- the whole garage will be dry walled and painted a flat white with wood base trim at the bottom.
You don't want wood base trim, either. It will take a beating and won't like the moisture. The new PVC and outdoor moldings that you can get these days will hold up famously for you. (They are a little pricey - its something you can always hold on until later, like the HVAC. No need to have the base molding in for the initial build.)
I'm guessing the floor drinks are good for water run off? With winter etc. never seen them before that's why I ask.
That and some people set aside car wash bays. Floor drains often come with environmental/permit nightmares and in many areas, grease traps are required. You definitely don't want to deal with those, or the maintenance involved. It's $$$.
The other thing with floor drains is that they collect flammable gasses, which are typically steered towards your garage doors via your sloped floor. IMO - floor drains in the middle of the floor are a safety issue to avoid. If runoff is a concern, you may look at putting slot drains at your garage door sills.
Max is 11 feet unfortunately :-/
This is going to relegate you to a 4 post lift or MaxJax. All the 2 post lifts I've researched require 12'+. The other thing to consider is your sloped floor. With the depth of your room, you are going to have nearly a 10" drop from one end to the other. So... a 11' max ceiling will probably be 10'-7" in the middle of the room. If you are attached to the house, you will also have to be 8" below your inside floor for a gas curb, so you'll want to make sure that is taken in to account also.
... Lot's of homework to do here if you want to have a lift installed. You also will want to plan out your concrete saw cut joints with your concrete company to make sure they don't put them in places that violate your lift install instructions.
They are installing theew 9' doors.
If you go any wider, you will be really heavy as they are insulated and when you get heated - larger openings will let out more heat. I went with 8' doors for better energy efficiency and now that I'm using them day-to-day, I really wish I had the 9's. 8 is fine if you have a straight shot at the garage, but its really tight getting a truck (and its Dumbo mirrors) through the opening.
Outlets every 4' seems like a lot maybe it's not though.
I think your logic is sound. For a machine shop, this might be good. Working on cars - this is a waste of money. Outlets and wire are expensive and are a total waste if you never use them. Conduit is cheap. If you think you might want more in the future, you can always run conduit, boxes, and then put blank plates over them for now. When you need outlets in the future, just pull more wire.
If you know where your workspaces are going to be, you can load up on outlets there. I suspect you'll be using hand tools and air tools mostly around your cars.
Don't forget to put outlet drops in your ceiling. If you get your lift in, you may want to drop electrical down to the lift and have a work center w/ outlets on the lift(s). You will probably also want your lift power to come from the ceiling.
People also tell me that the internal combustion engine will be illegal in a few years.

You may also want to run conduit to prepare for the possibility of an electric car in the future. Even if you don't want one, that could be a big plus when you go to sell the place some day.
No heating or cooling at this time, builder is roughing in a gas line to the garage in case I want heat down the road. I live in PA so heat will be a must down the road.
Run pex in your slab for radiant heat. The tubes are cheap and its easy to do when you are pouring the slab. The manifolds and system are expensive and can go in when you have the money for your HVAC. I watch TV every once in a while - I hear that our next President is going to make us all instantly rich, like him - so you shouldn't have to wait long.
You can read the threads and I can attest - radiant flooring in the garage is wonnnnnderful!
6" concrete is the minimum allowed for a car lift which I will need. (From what I have read, I could be wrong)
You'll want to research this more. I've looked at a lot of lifts and only seen requirements over 4" for commercial lifts intended to hoist buses, RV's, and fire trucks. So, you'll want to double check that.
You will want to add an inch to your lift minimum to account for variability in the placement of the final slab. (I assume you will also be insulating your slab, which will also take some precision out of the thickness...) Adding extra thickness for the sake of adding concrete is not necessarily a good thing because a thicker slab = more shrinkage stress, which will increase your likelihood for unwanted cracking.
I added the 220 outlets just in case (I doubt I'll ever weld or grind) but just in case.
This is an area where you will definitely want conduit. If you put in a 40A circuit and one day you find a need for 60A, etc. you'll want to be able to pull wires easily.
I'll ask the builder to do the small pockets oiie someone mentioned, that will help save money, that never even dawned on me to try that.
Intuitively this makes sense and it would be OK if concrete were a homogeneous (like iron) material. However, your slab is reinforced concrete which is a heterogeneous material. Having one area thicker than another puts differential stresses on the reinforcement. This will increase your likelihood for cracking.
^ Don't believe stuff you read on the internet. If you research this, you will not find a single slap spec from a lift manufacturer for a new slab (retrofit slabs are something completely different) or instructions in a concrete placing manual on making one part of the slab thicker than another.
This is more of a concern the more highly reinforced the slab is. (It probably won't cause too many issues if you are just using one layer of mesh.) However, the lift doesn't need it for strength and if your concrete company is careful and puts some gauges in place so make sure they give you the full thickness you are calling for in the are of your lift pads - you will be good.