94 gt 5.0 aode swapped to T5

Short answer, no. You need a manual computer or a chip that turns off all the auto functions. Getting a T4M0 computer is cheaper and easier.

It shouldn't cause a miss or buck at highway speeds, it will typically cause a bit of hesitation when it reaches the automatic-trans shift-points (due to the timing getting retarded). But at cruise it's likely not the transmission / computer setup. More likely a lean condition - as Mustang5L5 suggests a fuel related issue. Could be O2's, MAF, fuel pressure (pump or regulator or filter - easy enough to test with a gauge). Vacuum leaks or other sources of un-metered air (like the PCV system - especially take note if you have a cold-air-intake). A full tune-up is advisable - plugs, wires, cap & rotor, O2's if they've never been changed, clean MAF, change fuel filter, check fuel pressure. Listing any mods would be helpful too - if everything's in good shape it could be the car was modified but never properly tuned.