How common is it for the OEM wiring harness to start having intermittent connectivity issues?
The wiring for the coolant temp sensor has failed and more recently the cylinder position sensor wiring.
The car is a 1996 civic dx hatchback that has been swapped with a y8 over a year ago, it is also running a obd1 jumper harness.

 

Another thing that I have noticed is that when you run an obd1 ecu in an ek chassis you lose the proper ecu mounting positions, meaning that your ecu is now free floating along with a huge jumper harness behind the kick panel. I believe that this could be a contributor to my problem since this puts the wiring under more stress.
Does anyone make a product that would allow me to properly hard mount this ecu in my car?

 

The harness is 21 years old, the engine has been swapped and a jumper harness installed without properly securing the ecu. Sounds to me like wiring was pulled or not connected and reconnected properly. Whenever something like that is messed with and proper care isn't take when working with it, problems will arise. You can secure the ecu in the same location as the regular obd2 ECU, not all bolts may line up but it's enough to get it off the floor and allow you to put the kick cover back on over the ecu.