Can the OP take some pictures of the engine under hood and the wiring harness? Also a good technician can perform repairs to the wiring harness that unless you really studied it you could not tell where or what was repaired. I was once taught that a sign of a good mechanic is that you can not tell what he has fixed. Over the years I have fixed/repaired hundreds of wiring harnesses. Doesn't matter if it was due to rodents, fire, theft, or improper repairs(poor radio installs).
I'm pretty sure the OP will not be back, even though I wish he would.
We would like to help him out the best we can.
He's not happy because we've pointed out that someone has done something that shouldn't have been done.
He's under a false impression that the parts in question are stock part.
Sadly the damage done and it not starting are directly related.
And it's highly unlikely that just replacing the emulator will fix his issue.
He's not going to get help from any reputable dealer because the tractor is now a huge liability.
Altering emissions is a federal crime and the fines for doing it or not reporting it are super steep.
On the other side of the coin, sometimes we got to do what we got to do to keep our equipment running.
If the OP came back and asked some questions and answered some questions we might be able to help him get past this.