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As far as programming, that is why I went to some effort to try to find someone who has considerable experience at this sort of thing. Unfortunately, my guy changed jobs (or changed to a job where he is no longer the boss and owner) and is, basically, no longer available to me.
Someone that knows what they are doing (particularly on the brand of system that you have) can pre-program the computer, then, when (if) the engine is dyno'd can do some finer tuning on the course tune, then work on getting the starting/cold running parameters working well, then do some final fine tuning. Some like to do the latter on the road, while others prefer to do it on a chassis dyno. I am at the last stage.
If you are 'shooting in the dark', it may take quite a while, or, at worst, you could damage something. I have seen a thread (6-18 months ago) from a guy who was doing his own programming/tuning. He finally got it to run OK, but it appears that he probably 'went through hell and back'.
My advise is to get with someone who has quite a bit of experience with it and let them do it - saves a lot of time and worry, and, may not cost too much (couple of hundred $$).
I just made contact with another guy who is experienced with the SpeedPro units that has a shop a lot closer to my residence than my original guru. He prefers to use the chassis dyno. He thought that it would only be about $100 to do the final tuning since I am running pretty good right now.
The people who seem most likely to do this sort of thing are the ones that 'specialize' in the high performance Mustangs. In the Mustangs they usually put a supercharger or turbocharger on their modified 5.0s, but some of them do a lot of EFI applications with their cars, and you may find someone that keys in on your brand (Holley, or whatever).
I don't think that you can compensate for 'mismatched' cam/manifold. You can optimize the programming for your setup, but the setup may have some inherent flaws that cannot be corrected beyond a certain point. Everything is relative with these cars, anyway. (So what if you only get 500 hp. It's still a beast!).
So far, all of my programming has been static except for the last one where we were running around an industrial park. The more 'major' problems (and they weren't too bad) were corrected, but the real fine tuning takes at least a couple of hours on the road (by someone who is proficient at it). Since you can 'instantly' change to different performance characteristics on a chassis dyno, it should take far less time to do what is needed. But, I'm not entirely sure if a chassis dyno is 100% equivalent to an actual road test - haven't really talked to anyone about it. I figure that if it is not, I would be 99.9% tuned rather than 99.95% tuned (or a chassis dyno tune may be better - ???). But for the applications I intend for the car, whatever I get should be plenty good. I figure that I am 95-98% tuned, now, but I know that I will have some cold weather (that's less than 50 degrees in Houston) starting program revisions to do when the time comes. I had difficulties early this year.
I want to learn how to do the programming/tuning, but I think I can do that and get things to where they should be a lot faster if I let someone else do it, watch them, ask questions, then play with it a little afterwards. I want to be able to remedy a problem myself if I am out 'on the road' and something begins to act weird.
I've been trying to get ahold of Vern for several days. I thought he might be 'on holiday' before school starts, or both of them gone to deliver a car. He never seems to answer my messages or e-mails. If you talk to him soon, let him know that I have a couple of questions for him.
Hope some of this info has been helpful (or got you to look into some things more closely). I can't say that you will have troubles if you continue on your present course(s), but I don't mind passing along some info that I have gleaned from my journey along this 'not so well beaten path'.
Regards,
Frank
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