Microwave stop heating. Everything else worked fine (fan, clock, turn table). The HV Capacitor was taken out to see if that was the issue. Determined it was not the problem. However, it has not been put back in yet. All of a sudden the light, fan just starting turning off and on and eventually the microwave cut off altogether. After reading some of the comments posted, is it possible a bad magnetron tube is the problem? 
This is where I loose you. Are you saying this happen after you took the capacitor out or before. You may have blown the fuse.
Other than that I would think the magnetron tube is bad. This page will help in replacing it GE Spacemaker Microwave Magnetron Tube Replacement
It happened a couple of days after the capacitor was taken out. Didn’t even consider the fuse having blown. However, that makes sense. Thanks. Will certainly keep you posted on the outcome.
Keep it unplugged untill all repairs are made!