I have a code P1310 and some misfire codes for # 2 & 3. This just after I put the intake manifold back on. No misfire codes before that.

 

can mean either a random misfire or a misfire on cylinder #5. Given you just did work on the manifold, I suspect you are running lean due to an air leak (ie manifold to head or a vacuum line/intake tube where you worked is not totally sealed).