Try bypassing the operator presence switch under the seat. Just make sure you aren't bypassing the wires for the air seat. If this fixes your problem be aware that your operator presence will not work anymore.
I had the same problem last year when, after some use, the feederhouse would stop working. My local mechanic ran a live hot wire directly to the feederhouse switch, which caused the feederhouse to engage. Thus, I found that I had a weak ground going from the separator switch to the feederhouse that would get hot with use. He ran the wire through a spare fuse in the fusepanel and I was able to finish the season.
