I thought you would only be tuning the fuel and not the timing.
I mean you cant really tune the timing without modifying the dizzy. Just leave timing factory and get the fuel mixtures tuned.
I'd recommend connecting the EMS to a TPS. I'm sure it will have an input for it. The factory TPS is no good for aftermarket ECUs. Either find one off another car or purchase a Wolf 3D TPS, they are $70 or so and fit very easily to the 3t-gte throttle body.