I think you have replaced all the components you need to for fully functional flipper fun on your Flash. Except the part that will most likely be your problem.

http://www.rtbb.com.au/catalog/product_info.php?products_id=1245

This is the EOS switch stack that acts as the EOS for the bottom RHS flipper and routes power to the top RHS flipper. If this is not adjusted, then you can have all sorts of issues, such as low power and the "hammer effect" you describe.

I'd start with replacing the EOS and see if that improves things - but keep in mind, they are tricky to adjust.