Thanks everybody for the responses let me make sure I am understanding everything while explaining a few things.

First off the reason the pump fuse(s) we're removed was to jumper the connections, I only had a paperclip to use and I couldnt get it to stay put with the fuses in place. Fuse 6 doesn't matter, I thought one controlled the intake pump the other the main pump?

Secondly, I'm guessing the shop was just impatient and either
A. Didnt think they would make any money off of a simple relay swap.
B. Didn't want to work around the cars quirks. (passenger side door would'nt open, air intake duct missing, drivers door handle broken...)
C. Really, Truely don't know what the f#$k they are doing.

This being said if I still have a few remaining questions.

1. The car won't run, or won't run very well with just the fuses jumped, correct?
2. The car will run with the fuse & relay bypassed (jumped 3 way)?
3. The air duct between the air sensor and throttle body is gone, how will this affect how the car starts/runs?
4. What and where is the 25 amp blade fuse?

Thanks again...after we get it running i'll surely be back to sort out her quirks, but thats what gives them character, right?