I bought a 94 LT1 Camaro and it’s a great car but my trans started having issues and I let it sit for a while. One day randomly my friend wanted to attempt to drive it to see how it would act so I let him. The trans will only go to 2nd gear and won’t go to third (auto) but during the drive a noise came from the engine and the car shut off. Eventually I was able to start it and now it has a knocking noise but the knocking goes away under 1k rpms. Is this rod knock or something else

Sort out the trans problem first, may be related to the noise.

Have you scanned the PCM for codes? With the electronically controlled 4L60E there are many diagnostic codes that can set, and they don't turn on the SES light.