Computer upgrade options for 95GT

I have made many performance changes to my stock 5.0 engine. Started by stroking it to 332cu in with new crank, rods,and pistons in the machined stock block. Added new GT40 heads, valve train, and intake. Followed with new 65MM throttle body, 30# injectors and new fuel pump.
I called Ford Racing tech line about tuning my computer. That chip is not programmable through the data port. The only option given was to send upgrade info to a company where the would program a new chip and send it to me. I'm not to crazy about this idea, because if it's not correct or I make more changes I have to pay to reprogram every time.
So, what other options are there? Can I change to a 96+ computer that is programmable? Are there programmable replacement computers available? Are there programmable computers that plug in inline with stock and intercept the sesor data and allow tuning?
Any help would be appreciated.