Early pinball machines (of every brand) that have directly controlled flippers using the EOS to break the high current circuit, rely very heavily on accurate and careful cleaning and adjustment of the EOS switches. This is the most critical part to having flippers working well in these machines.

You need to adjust the contacts close enough to shunt power to the pull side of the coil as long as possible BUT make sure the EOS is able to open reliably at the end of stroke to prevent burning out of the coil.

Naturally there are many other considerations such as flipper bush wear and plunger/sleeve wear but, as you have replaced all of these, it probably comes down to SUPER critical EOS adjustment or replacement of you haven't already?