OK update.
First off I didn't get electrocuted once this time I"m proud I"m usually really good at that.
I busted out a couple of timing lights. You know those old ass things they used on mucsel cars in the day. First like any good engineer would do was gather base information. So I watched the timing with the stock ignition system on the car, and took notes on where the mark was at different RPM's idle, 2000, 3000, 4000. then of course we ripped it all out to install the new stuff.
Side note the bolts in our cars are the cheapest thing ever made if anyone knows where I can get a bolt kit let me know.
Couple of Brooklyn Browns later we have everything in the car and wired back up again. It doesn't take very long to get everything reconnected now that I have all the male and female ends installed. Doubled checked the wires like 3 times and started her up. To be honest the starts are a little rough and I now know why.
I started to check the firing on both banks as I did before and noticed one major thing right away. Channel one is firing what looks to be twice as much as Channel 2. Now I can't count that fast put it is am asumption that I am sure is true. If you compare Channel 2 to stock, the rate at which it fires looks identical, which is good. I switched some wires around so that the trigger for Ch.1 is now the trigger for Ch.2 and vise versa. Changed the plug wires around and now got the exact same results. Channel 1 (now trigger 2) is firing twice as much as the other.
This leads me to believe that I have a box that is broken. This is concievable because it is an older used box. I would still like to get my hands on an ociliscope to check the trigger wires to make sure that they have nothing to do with it before I buy a new one.
You could tell that the car was trying to conrol the timing (back to Trigger 1 for Channel 1) because if you watched the mark it would start around 10 and just advance advance advance then go back and do it all over again. It would advance to the point that was normally about where 3000RPM was stock. It was doing this because it was basically just continualy firing and it couldn't find the proper timing for the spark because it just kept going off.
I think that once I prove to myself that it isn't the trigger wires (which I reall don't think it is its just that a new unit is a chunk of $$ that could be going toward suspention) I will buy a new unit install it and everything will be gravey. I could send this one back to MSD and get it fixed but I don't want to wait that long. If any member has a unit they could mail me so i can test it I would be happy to compensate you for it. I just don't want to spend another 400$ right now I just spent 600$ on the TV for my car. We are one step closer though.
Note stock ignition is back and and car runs great.