It is recommended that the intake manifold bolts be replaced when the manifold is removed and reinstalled. There is a good reason for this; it probably was found from experience that the original bolts stretch when tightened; and then will be too long to seal properly if they are reused. It also could be that the aftermarket intake gaskets are thinner than the original parts; and require shorter bolts as a result. Whatever the reason; I have found that problems occur when these warnings are not followed. They don't make you buy $27 worth of bolts and washers just to make a profit. I expect you have major vacuum leaks at the lower manifold as a result.
The fuel injectors for the 360 engine are a different part than the 318 injectors. This usually means the 360 injectors have a larger orifice size. Using the 318 injectors on the 360 motor will make it run too lean; which, when combined with vacuum leaks at the manifold, causes the symptoms you are describing.
I would also check the ignition timing with a timing light. It often turns out that the distributor drive gear was not meshed properly when the distributor was reinstalled. The other common problem often is that the position of the plug wires in the distributor cap was altered when the wires were installed; which could keep the correct firing order; but make all the wires one position retarded.