My car came with a/c i removed the a/c and rebuilt the engine and used a timing mark idicator off of a non a/c engine that is on the left side not the right does the computer know this? Would this casue my engine not to start?

From your user name, I assume you have a 280Z? The location of the timing indicator should not matter as long as the mark on the crank corresponds. When they installed the A/C, they moved the indicator and added a score line on the crank to match. If you move the indicator back to stock, you need to use the factory score line on the crank. Also, did you line up the distributor properly? With the timing chain wheels at their TDC position, the rotor should be pointing straight at the #1 spot on the distributor cap.