Got the Jeep back today!
In the end, the total was $1,225.
Brake pedal is nice and stiff now like it should be. Said the plugs were totally shot. That cone air filter wasn't doing anything anymore and put it back to stock. Throttle body was just covered in gunk (showed me the pic he took of it - yikes...). Headlights are WAY better now.
Also did a few things for me for free - painted the top of the engine black when he had it off to replace the valve cover gasket, cleaned up the engine, fixed the door retainer thingy that broke in the wind about a month ago, replaced the thermostat that the shop put in with a 180 thermostat (shop put a 195 in), and replaced some plastic rods/connectors (don't remember the names) with metal ones.
Driving it I could immediately tell a difference. Felt taut, didn't roll in the turns, engine was smoother... Felt like a new vehicle!
Even gave it a going over with a Mitt and some soap.
Turns out the guy is a Marine vet from the jungle era. I mentioned I got the loan for this one from USAA and asked if I was in, so we swapped some stories and a healthy dose of mutual respect. Good man doing honest work for an honest price. Can't ask for anything else.
All in all, supremely happy. Jeep feels brand spanking new.