1996 4.3l Chevy Possible ground issue or Computer problem?

I installed a 1999 chevy 4.3L engine with a 1996 chevy manuel computer in my 1947 Willy's project. I have borrowed a OBD II scan tool which was working while I was trying to figure out why my engine was running rough and very rich, I replaced the plug wires, the plugs, the front O2 sensors and the fuel pressure regulator chasing the problem. The engine is still running very rough rich smell of gas and some small back firing. The scan tool won't read now either, so I found that I had not grounded the wiring harness and the block so I did that, it still is not comunicating, the scan tool either says waiting for information or when you go to engine controls the scan tool says the engine controls are timed out. Is it possible I did something to the computer by not having it grounded properly? Or maybe I don't have it grounded right yet? I grounded from the body to the frame and from the same point on the body to the block and from the same point on the block to the same point on the frame and then from the same point on the frame to the neg terminal on the battery, I attached the ground wire coming out of my wiring harness to the same spot on the firewall I grounded to the frame. The wiring harness is a custom harness for these type of applications. Thanks for your help in advance.