Welcome aboard!
You've come to the right place. 1st off, ignore the "Here be Dragons" wording of the Haynes manual. It's rubbish advice. Everything that you'd ever want to know about the wonderful MFI system is right here in the
Pelican Technical Articles section. It is perfectly possible to tune and adjust your MFI and it's really no more difficult then tuning carbs. It's just different. The important thing is that there is nothing that you can do to the injection system that will generate more HP in your stock engine beyond making sure that it is functioning correctly and tuned correctly. Your car's MFI system is essentially the same system that was used on the 906's, 908's and 917's with a few sub-systems tacked on to help it run well at idle. Unlike later injection systems, none of these enhancements hurt the top end performance in any way! Focus in on the Check - Measure - Adjust document (CMA).
1) First you need to size up what you have. Are all of the hoses there?
2) The symptoms that you describe sound like someone has mucked around with the system and possibly disconnected the cold-start and cold-idle systems in the interest of "improving" the MFI. They failed. It's a common "upgrade" which is done to The systems are there for a reason and disconnecting them doesn't make anything better.
3) The only "modification" which is generally recommened for the early MFI system is to disconnect the cold-start system that trickles fuel down the stacks -- it's a fire hazard. In the case of my car (also a '69E), there is a simple switch that you can add which will peg the adjustement rack to full rich when cranking the engine cold which works a lot better and doesn't risk an engine fire.
4) As far as improving the driveability of your car, I'd recommend you check into an MSD ignition system. It makes a pretty big difference in the 2-liter engines and less of an impact in the later engines since their combustion chamber is better designed. The multiple sparks do wonders for improving the engine's part-throttle transition in the 1500-3000 RPM range. Above that engine speed the system doesn't perform any better then the factory electronic ignition system.
Be sure to post pictures. Are you registered on the
E-Registry?