Not Shifting Gears

After getting my heads resurfaced along with other minor fixes I left the shop and immediately my truck was struggling to change gears. It changes from 1 to 2 with ease but it gives a small jerk when it shifts. From 2 to 3 it struggles more and the RPM's reach over 3,000rpm and it will still not shift. It only shifts when I let go off the gas. It bogs really bad when I punch the gas. The easier I accelerate the better it is but still not normal. The muffler sounds different than before similiar to a honda car with performace mufflers. Not really but it has a odd sound to it. My mechanic thinks it's the transmission. So I took it to the Transmission shop and they think it's the catalytic converter. They cannot be sure because not enough power is going to the transmission. So I had a new catalytic converter put in and still having the same problems, better but my truck is still not acting right. The truck starts and idles fine. A Transmission mechanic told if it has to do with power then it's not my transmission. The codes I get from auto zone indicate the knock sensor and a EVap leak or some sort of problem but none of the codes are for Nissan. I took out the EGR Valve and not alot of carbon was present I cleaned it anyhow. And still no luck. I replaced a hose leading from the egr valve to a black plastic circular part. It had a small hole. So as of right now I'm stuck and don't know what to do. Any help is appreciated, Thanks, Danny