The J6 hack on the interconnect board is very common on system 11 machines. I suggest replacing the header pins and the connector. Use trifuron molex terminals.
CPR is taking "pre-orders" on Diner playfields...
http://www.classicplayfields.com/order.html
CPR also offers a mirrored backglass to replace the original tarnslite...http://www.classicplayfields.com/photo191.html
I have one of the backglasses. It looks great, but I haven't had the time to install it.
Congrats on getting a Diner. To me, it's one of the best system 11 pins out there. It's also has very pretty artwork.