Update:
Bike still wasn't idling correctly, no matter what I did. Then it wasn't getting fuel. I took the carbs off, took the float bowls off to ensure nothing was gummed up. Took the fuel lines off and blew out the filters, they had a little bit of stuff in them which is what I expected because after I cleaned the tank there was some residual particles I couldn't get out. Then I removed the petcock and it was a bit more gunked up, so I cleaned it real well and got some more of the rust particles out of the tank, rinsed and dried and put in fresh fuel.
With the carbs off, I noticed that when PJ had them, he replaced a throttle shaft plug, but not both. The one he had not replaced was sort of beat up, and had a dent in it and was a little beat around the edges so I took the chance and put some silicon over the plug and made sure there were no air gaps..... put it all back on the bike and started it up, idled high for a minute or two then right on down where it was supposed to be.
So now, like trek told me to do I will sync the carbs once I get the opportunity and take it for a ride! Thank you all for the help