My VCT is now way off timing. Prior to that, my engine misfired at highway speed of 70MPH then the Engine Check light came on. I changed the spark plugs and wires. The gap may have not been EXACTLY correct. Two weeks later, the engine started acting up. There is a major acceleration hesitation and stalls every now and then.

Could my changing the plugs and wires myself created this problem and what should I expect???

Check to see if you pulled the VCT connector loose by mistake. It's right in front of the #1 spark plug. Hopefully, you didn't damage it by hitting it with a tool!