It might be my imagination, but since you mention it, it does sound like there could be some metal-on-metal contact, somewhere. I read your thread about air-hammering the valve covers to make them work.
Are there taller covers that will clear the alternator and intake? Our heads have the std. sm block ford bolt pattern, so any cover will bolt up. What are the guys at corral.net running with 94-95 Stangs that have roller rockers?
Also, exhaust leaks before the O2 sensors can cause problems, as the EEC-V relies HEAVILY on their input.