89 5.0 GT- Can tourqe boxes be worn out through regular use?

Welcome, Sanchez!

I agree the the karthief....subframe connectors is a great starting point. The fact that the previous owner installed new uppers and lowers does not affect the torque boxes.

Torque boxes do not really wear out, as they are welded in from the factory. The only things that would affect torque boxes would be 1) rust, and seeing you are from CA, that shouldn't be a big issue, or 2) high RPM launches on slicks. Considering the car did not have subframes installed when you bought it, I'd say that you are fine as far as that is concerned as well. Many of these cars have been used and abused, all without subframe connectors or torque box upgrades.

From what I have read, you should be fine to take it out and enjoy it as it is (once your maintenance issues are finished).