You can hook the factory dist to it, I was planning on removing the stock computer and harness. I just wanted plug n play and to control timing from the holley as it was intended, not piggy back. I'm over piggy back systems on my stuff if I can help it. Setting timing on the hyperspark is way easy. Drop it in at 0, put alignment cap on, mark #1, slap cap and wires on - should be right on the money, trust but verify.
I heard the same thing about the manifold - that is why I run a 1 inch open spacer, but it means I had to run a short 2 inch air filter to clear the hood pad. I never ran it without the spacer.
I did the fuel pump when I bought the truck, just wanted the vortec upgrade, so far it has been ok, I bet I'm on the edge of hp for the 96+ vortec pump.
I like the throttle extension, but have to grind/clearance the fast ez efi bracket, easy, just takes a few minutes and rattle can it black.
Make sure to buy that tap to clean up the water jacket threads on the weiand...
There was more to the build, I might make a new concise thread, ie, you cannot buy the oil cooler line fitting plastic diverter basket, you have to buy the 96 up fitting and then move the plastic over to the TBI version of the fitting. That was fun.