It also deleted the "For E36slide" from the title?
If you read the first line, you would know that he cannot use his legs.
TheEaton that comes stock on the Cobra can easily be ported, and with the stock transmission and IRS, they run mid 10s. So are you trying to say that the transmission is why it goes into the 9s, and not the additional horsepower? You think that the Whipple doesnt make the power, or do you think that you need more than 700hp to hit 9s?
When you say "have Ford modify the transmission", it makes me wonder if you have ever done any performance work to a car - ever. You can't just call up Ford and have them make a one-off for you. Your only realistic option is to go aftermarket.