Seems as tho that vacuum reading is where this issue is. But there are many reasons that it might be low. Since you changed the manifold, I'd go there. I agree that a 4 degree change in timing will not change much but the timing chain "line up" issue does need to be changed. You are going to have to open it up to check all these items. Pull the manifold and ck for leaks, check cam for wear (possible lobe going away). Redo the timing chain or get a new one and degreee cam. Put it back together and run again.
Fuel line is ok but make sure that your fuel pump is up to par. These are difficult things to check but all must be done. There is not enough vacuum and you need to check why. The fact that the car got slower as the day went on does point to an issue. I should be running better and winding up better that it is.
There is alot to check but if you want to solve the issue I don't really see another way. I helped 64Post with his issues and we are still chasing the problems. Just my