Multiple codes after engine swap

I recently had a new engine put into my Silverado. Right after picking it up I started to get a flashing check engine light at highway speeds around 55 to 60 MPH only. It would stop flashing when I slowed down or stopped. The only code I was getting was P0300 for multiple misfires. Eventually the check engine light came on and stayed on now in addition to the P0300 code I am getting the knock sensor code 4 the bank two knock sensor. I checked the resistance of the knock sensors, and both are within spec. The engine is under warranty, but I've already brought it back to the mechanic once and he said it had nothing to do with the new engine. He changed a bunch of other things, charged me another $2,000.00 and didn't fix the problem. So, I decided to fix it myself.