I've been slowly looking into this also, I'm going to use a 5-speed so I dont know anything about the trans controller. However, for the engine side, I personally was going to go with a simple one, the fi-tech non-spark controlling model, then use a GM HEI distributor. I will need to upgrade the fuel pump to a higher PSI pump and use a carburetor intake manifold.
As far a gauges, they all should still work if you still go through the stock computer for that aspect. Again, I dont know about eliminating the stock computer for the auto trans but for the manual I believe they all should still work since your not eliminating any to use the stand alone efi system and the GM HEI has a port for the tach.