Engine Trouble Please Help!!!

[BLACK AND BLUE 67-72]

This last weekend my friend and I changed his intake and carb, the intake is an Eldebrock Performer RPM and the carb is a 1406. The problem is that the engine sounds like it is misfiring at about 3500 to 4500 RPM'S, It varies because it doesn't do it all the time.Also it feels like the engine is bogging down at a certain RPM. We marked the position of the distributor and placed it back into the same position, placed a timing light on it and the engine is in time, it starts and runs great other than that. The engine has new plugs and wires and a new cap and rotor. Could it be the spark advance or the weights in the distributor, or the pickup coil, or something else? Please Help!! Also a question about the vacume line for the vac advance on the distributor, does it go on the full or timed port ? Mine was hooked to the full and ran fine but a friend of ours said that it is supposed to go to the timed port, so I switched mine and it kinda feels like it has more power, or maybe it's just me.