so I replaced cap rotor, sparkplugs and wires . Cleaned the throttle body and the air idle control
new cam sensor new crank sensor, started it and it ran great...for about two days now it is missing at lower rpm's.
give it some throttle and it straightens out until it shifts into high and the rpm's drop and were missing again
no codes. Any suggestions?

 

Disconnect the front O2 sensor, see if it changes anything. (both, if you have two front sensors)

 

I will try that, I was also wondering if it could be something like the EGR system

 

98 doesn't have an egr, Did you double check the wires that they are on both the plugs and cap securely? If it's amiss at idle you can pull the wires off one by one to find what cylinder it is. Definitely helps to put some dielectric grease on the boots to help with installing and removing.

 

thanks for the idea and I already checked all that ,
now its throwing a code for the output sensor on the transmission I am not a transmission person other than swapping them out
will the speed sensor cause this

 

No, speed sensor won't affect how the engine runs.