Wow there's a lot on that list... It looks like he wants to do a ton, is the car in bad shape? Lots of miles?
I'd find out the source of the click or clicking and probably get on that first if it's serious. Maybe a CV joint?
Seems like he wants to put new mufflers on, $300 for new flowmasters from the write up.
The throttle body service? Is he just going to clean it out? I usually clean mine with some carb cleaner and a rag, when i pop out my air filter to clean & oil it, I usually pop the intake off and clean up the inside of the TB and butterfly valve, it keeps it nice and responsive by keeping the carbon and build-up off of it.
$129.99 for an EFI service? Is that like seafoam-ing it? Seems a bit steep honestly, but please correct me if i'm wrong. A can of seafoam is less than $10 typically and can be done easily, just be careful not to do too much too fast.
Brakes are an easy one to do if you're mechanically inclined, or have a buddy whom is that you can get to help you do it. For that, you could put new brake pads and rotors on, possibly all four wheels.
The clutch...$980? Is THAT a good price? I haven't had one done in YEARS so I don't know honestly. If the TOB (Throw Out Bearing) is squeaking, is that impending doom? Possibly...I'd make sure my AAA membership is paid up and start saving for the whole clutch to be replaced, but I wouldn't do it until it fails personally, but I have 2 cars and wouldn't be put out if one was down.