http://i50.photobucket.com/albums/f313/torygrose/Mobile%20Uploads/20170620_184625_zpsyyzhogye.jpg

http://i50.photobucket.com/albums/f313/torygrose/Mobile%20Uploads/20170620_184633_zpswldrzsnm.jpg

http://i50.photobucket.com/albums/f313/torygrose/Mobile%20Uploads/20170620_184625_zpsyyzhogye.jpg

Tgrose wrote:
Do these pictures mean that my AIS is out?

Yes

If yes,should the tube coming off my intake be plugged? Because it is not

Yes it should be sealed.

Doc

Tgrose wrote:
Do these pictures mean that my AIS is out?
If yes,should the tube coming off my intake be plugged? Because it is not
Also I located an air leak in the manifold at the heads and I'm going to pit permetex on the joints to seal it


There is a certain type of Permatex that you need to use. It is called Permashield, IIRC. It is like Hylomar. It is a blue non hardening sealer that is heat and fuel resistant. You want to avoid a silicone type of sealer that might cause the flanges to distort. The Permasheild, will flow as you tighten the flange bolts. Just apply the sealer to the surface around the outside of the orings.
While you have the manifold off, surface the flanges with some sand paper and a flat surface like a granite or a piece of thick glass. Put the paper(320 should work) on the flat surface, and work the flange face down on it in a figure eight motion, until the flange face is clean flat and even.

Like Doc said, yes. You need to plug that line, or when you take the manifold off, you can sweat the port shut, the same way a plumber sweats a copper fitting. That way it'll be sealed completely and permanently.

Ok got it plugged, cleaned and sealed, it appears the problem has been resolved! Thanks for all the help, couldn't have done it without this group. I'm just glad to be back on the road again after 3+ months of crap going wrong!

Good. Resist the temptation to turn your idle back down, now that the bike is running decent again. There is about a 45 pound crank wallowing around in the motors guts. When you turn the idle way down, that thing ends up thrashing back and forth, instead of maintaining some semblance of order and steady smooth rotation in one direction.

Check the secondary idle jet....when you take off your air cleaner there are two holes on the bottom rim of the mouth of the carb. The one on the left is the secondary idle jet. push a pin through it. If your idle goes up you found your problem. I have a 2000RSS that had this issue. My plugs were black and the rear was fouling. It also makes your mileage suck. I went from 28-34 MPG to 43 MPG!!!