Thanks I sure will. Bike is still in NJ hopefully I'll have time to go get it this weekend

 

Is it possible that you have the actual codes that were displayed either in your paperwork or written down somewhere as that may help narrow things down.
Please don't get the harness just yet until you've checked some things, by all means locate one etc but I've yet to see a whole harness needing to be changed for a sensor code, repaired yes, but not replaced.

Was the vehicle speed sensor checked by the mechanic do you know? This can cause idle and some running issues although not like your wide open throttle and chugging example.
Was a fuel pressure test carried out?
Are you able to access speedo diagnostics? A search on the forum expalins how?
Is the problem still constant and displaying the same codes? Make a note of them. The first thing to do then is clear the codes, run the bike and see what codes come back.
Let us know what they are.
Is there any point when the bike runs fine?

All your sensors I believe share the same 5 volt power supply and also have shared sensor ground. It is typically only the signal wire that is independent for each sensor.
Quite often a problem can lie in either that sensor power or ground wire and cause all manner of issues and more likely to cause two sensor codes like you had rather than both those sensors failing at the same time.

For example, I've seen on more than one occasion, although not often, when the wiring for the jiffy stand sensor got damaged/frayed where it follows along the frame rail near the rear rubber mount. This can cause very poor running but no code is displayed and would seem like a unlikely candidate for causing poor running as it's only a jiffy stand sensor right? However the power wire and earth wire going to it also goes to other sensors on the bike and was causing them to give false voltage information to the ECM.
It was this that caused the poor running, stalling and false codes to the ECM


So irrelevant of what the previous mechanic said, you now have the bike and should start back at the beginning and start with the simple things. Then you know it's definitely checked off the list of probably causes.
Some of the checks are unlikely to solve your issue, but it's a good way to start as there is nothing quite like spending ages chasing an electrical issue, only to find a loose battery terminal which should have been checked first thing.
If you haven't already, think about getting a service manual. Mr Vernal's pictures above give an idea of what is in the Electrical Diagnostic manual and although expensive, they're cheaper than a wiring loom.
A photo can be useful to make sure things go back in their original locations.
Try some easy things before getting into the nitty gritty of fault finding. But if you find you do have to delve deeper, be methodical.

You have gas in the tank and it smells right?
No recent mods to the bike before the issue that might be related?
When the problem occurs, are you getting good spark front and rear?An inline spark tester would show this.

Check your battery lead connections, both sides. The main ground wire at the transmission mounting point should have a thick and thin wire in a heat shrink tubing. Check the thin wire isn't corroded and it's secure.
Check your sensor and secondary grounds, very important, located to the left of the battery on the frame in front of rear fender. Must be secure and clean. Put these wires back on the same posts they come off of.

Do the other functions on your speedo still work? Toggling between trip and clock etc? Does the speedo still display the rpm?

The engine temperature sensor is secure in the front cylinder head?

A relatively basic way to take sensors out of the equation is to disconnect them one at a time and see if it improves your original running issue. It may cause some other symptom, but does the initial issue improve. Remember to clear any codes caused due to doing this so they don't confuse things.

I could kinda go on here but hopefully you get the idea.

Good luck

 

Thanks for all of the info and guidance. I dont have the bike yet I'm picking it up on Monday and I will start from the beginning and do my own tests before I go out and buy a new harness as per your advice. I'll keep you guys posted with what I find out

 

Personally, I would start with checking the grounds, more likely a screw backed off and a low power "clean" ground is bad. After looking through the Wiring Diagrams I noted that all of the sensor grounds are coming from the ECM itself and not from a separate ground (P78B-2 Pin 7), check continuity from that pin to center pin (pin 2) on the TPS, plug the ECM back in and check for continuity to ground at the center pin of the TPS (pin 2). If the first check is good and the second is not then question the ECM itself because Ground is not going through it for the 5V sensor ground.