My 2007 Honda Element has a mint body and interior and under 64,000 miles but due to its age it needs about 4k in work, here is the list

New tires, front struts with dust boots and bump stops, rear shocks, alignment, water pump, universal belt, front lower ball joints, outer tie rod ends, timing side engine mount, rear brakes, flush and bleed the system and emergency brake adjustment. Should I do the work and keep it due to low miles and good eyeball condition?

Before I committed to these repairs i would take the car to two more shops for estimates. There seems to be an extraordinary amount of work on such a low mileage car. It may be your mechanic is greedy.
Tires yes, but the rest is what you might see on a high mileage car. Trust no one where money is concerned.

Fix it and don't neglect your car going forward. In all likelihood some of the problems you're having now were caused (or at least aggravated by) your lack of fixing other things in a timely fashion. For example your front suspension components surely contributed to your tire wear. These things all didn't go bad at once. I do agree with Barnes on getting a second opinion however.

You sure DOG a car, don't you! All that didn't just spoil with age. Have it fixed and take better care of it.

You are getting scammed! There's NO WAY all those things would be worn out at 64,000 OR it has been clocked and the odometer has been tampered.