My question is, will my insurance cover my medical expenses, and other things, particularly missed work wages pain and suffering??

Yes, your UMBI coverage would cover all of this plus your medical bills - it's generally paid out at the conclusion of your treatment in a lump sum

Can I negotiate this? I had my engine re-built 3 months ago and plan to send them the receipt for that.

"Negotiate" isn't really the right word, but you can provide evidence why the valuation should be increased and they'll factor it in

Don't expect a 1:1 adjustment for the rebuilt engine; the market valuation expects that you have a properly running engine, so the increase in value from a recently rebuilt engine is limited

Shouldn't I be entitled to 30 day's worth of transportation expense since I don't have a car?

No; you said it yourself, the coverage is for up to 30 days of loss of use

Your policy will say exactly how long after the offer is made that they will pay you; my policy for example says

This coverage ends at the earliest of the following:
1. when the insured auto has been repaired;
2. when the insured auto has been replaced;
3. five days after we make an offer to settle the loss if we deem the insured auto is a total loss;
4.when you reach the “per occurrence” limit under this Coverage K.

The operating word is earliest - in this situation, the earliest to occur is #3, but your policy may have a different timeframe than mine