Buying a manual for the car is the first thing EVERYONE should do so lose the attitude. That is how you learn alot about the car itself and how everything works.

So lets go back over this then, your original post is a little unorganized.

Car ran like crap, back firing and hesitating.
fixed vacuum leak, replaced basic ignition stuff and timing chain
replaced fuel pump and fuel fitler
got the car to run and reset the timing correctly

Have you looked at a wiring diagram for that MSD box to make sure its all hooked up correctly?
Have you checked/reset the TPS?

After all of this how well does the car run now?