45psi will not likely damage anything or cause poor running. 90psi could cause pump seals to leak. Low pump pressure on the other hand could limit fuel flow to injectors.
I would revisit all other adjustments, throttle, air, and ignition. Make sure all air hoses and seals are intact.
Follow the pump PDF to adjust linkages from pedal to throttle body.
Adjust your timing to be all-in around 3k rpms.
Intermediate shaft, air/fuel screw and idle screw are the final adjustments which should dial-out rough running. An AFR also makes this step more scientific than adjusting by "feel".