Thanks for the Jets-R-Us info.

I will try to get some pictures this week. What exactly do you want pictures of?

I haven't had a chance to take a closer look at my idle screw, but I do know my needle jet is brass, and I have one brass slide needle with 3 adjustments for the e-clip and one silver slide needle with no adjustment.

It looks like Partszilla like ohiomoto mentioned will sell the needle jet, slide needle, and idle screw but they're pretty pricey.

I'm at about 900ft elevation so I figure going up in jet sizes probably isn't necessary right now, but since they're cheap I might just get a couple options like Paul suggested. I'll look into ordering those more this week as well.
Would you consider a leaky muffler a "free flowing exhaust"?  

The exhaust leak is the air intake leak’s less ugly cousin.  You should probably get that ironed out before tuning the carb.  Tuning the carb to a leaky exhaust system adds an extra layer of fun.

The different needles you have demonstrate the inconsistencies you’ll find in aftermarket generic kits.  Did you save the original needle?  Do you still have the white spacer that goes on the needle?  Have you swapped out or shaved down the white spacer.

I’d skip Partzilla for carb parts (more generic stuff I’m guessing).  I haven’t looked recently, but JetsRUs should have the correct needle for the carb.  I think they are like $20 each.  They have an entire section on the website for needles.  They are proud of those things.

I’ve bought the cheap kits before and found some of the parts usable.  I did compare the needle in one kit to an OEM needle and the needle taper was about the same (surprisingly).  I obviously can’t speak to the needles you have in your hands.

The only source for the needle jet, slide needle, and mixture screw will be OEM.  They are special parts unique to the LS650.  Sometimes ya just gotta bite the bullet.  It's a good lesson.  Never throw old carb parts out until you know for sure it runs correctly.  In the case of the needle jet, it is made from stainless steel.  I don't think you could ever wear it out.  It's very expensive, so cleaning it up is the way to go.

Lucme, pictures of your needle jet, slide needle, and mixture screw would be most helpful.  If there are any markings on the needle jet and slide needle it would be great if you could focus on the markings.  Some pictures of the carb interior, float bowl interior, enrichment plunger, carb exterior (right & left) and slide also will be helpful.

Regarding the leaky muffler (I'm lovin that comment about weight reduction), is it a stock LS650 muffler?  The stock muffler is very restrictive.  Unless the rust holes are in the forward chamber, I doubt that there's been much change in flow.  Pictures of the rust holes would be helpful.

Understand that we don't know if your issue is the jetting or something else.  The point is that you wholesale replaced the parts with parts that might be suspect and you need a known good baseline.  

But you are in good hands.  This forum has a strong record of helping people work through these issues. There are some incredibly knowledgeable people here.  

I'm just a POM (Plain Old Member).  I just wanted to point out the problem with the jetting situation before you invested more time into this.

 

   

The white spacer has been installed the whole time.

EDIT the links did not work. what is the best way to insert images. I tried using the function above the text box and used flickr links
EDIT 2 ok im just gonna use straight links so hopefully that works for you

Here are the pictures: (hopefully these links work)

https://flic.kr/p/2q7GJej
exhaust leak is coming from inside the sheet with the holes. I can't get to it to find or repair it without cutting it apart.

https://flic.kr/p/2q7PaQV
My 2 slide needles. The silver one has 5C39 marking. The brass one does not. As you can see the white spacer is not so white anymore. I ordered a new needle and spacer just to be sure.

https://flic.kr/p/2q7GJdn
Mixture screws. The one on the left is from the AllBalls kit. Same issues happening with both. Ordered a new one, as well as the spring, washer, and o-ring.

https://flic.kr/p/2q7Mpe4
Inside slide and diaphragm. That is how I have the holes lined up, which seems like its correct thanks to Dave's info.

https://flic.kr/p/2q7PAmK
Outside of slide. It's definitely seen some use but I didn't think it's too severe so I did not order a new one.

https://flic.kr/p/2q7NFgj
Top of carb with slide removed. Front of bike to the left. You can see the choke is pushed in.

https://flic.kr/p/2q7GJ7v
Inside bowl.

https://flic.kr/p/2q7NFgp
https://flic.kr/p/2q7PaFG
https://flic.kr/p/2q7PaEj
Some mediocre pics of bottom of carb. I didn't want to pull it all the way out since I can get at everything with it on the bike and it's a pain to put back on.

https://flic.kr/p/2q7PaBJ
https://flic.kr/p/2q7PAe5
Needle jet. No markings on it. It does have emulsion holes. I ordered a new one.

https://flic.kr/p/2q7PaEp
https://flic.kr/p/2q7NFbz
Choke or TEV. It looks in good shape so I did not order a new one.

https://flic.kr/p/2q7Mpfw
https://flic.kr/p/2q7PArz
Carb sides before I removed the throttle cable etc to remove the TEV. I do have the bowl vent tubes, I just removed them to take the slide out. The hose with the bolt stuck in the end is how I plugged the vacuum port for the stock petcock. The bolt is sealed with rubber sealant.

I ordered all new main, pilot, air 1, and air 2 jets. I got a couple different sizes as well as OEM sized mains and pilots.

If you want anymore info or pics let me know.
Thanks everyone.

The mixture screw you show on the left side of your picture has the correct geometry.  It is short like it should be, it has a straight unthreaded section for the o-ring/washer/spring, and the tapered section looks pretty close to the correct size.  The picture you provided of the side of your carb shows the mix screw deep in the hole like it should be.  I believe you said you ordered a new OEM mix screw, so when you get it do a comparison and let us know if the AllBalls part measures up.  Where did the bogus screw come from?

The stack you show is correct.  Spring on first, then the washer, then the o-ring.

The bad screw was from the Amazon kit (shocking, i know)

Its gonna take a little while for everything to get here but I'm going on vacation next week anyway. So I'll report back once parts have arrived and I've installed them.

Looking at everything now, I suspect the needle jet is a culprit. It also came from the Amazon kit with the bad screw and unmarked needle.

Mike, you clearly have more experience with these things than me so I'd like to take your word and get a brand new slide, however they're almost $200... So maybe I'll see if I can find a used carb with a decent looking slide. I'll look into that this weekend.

The brass needle jet is questionable.  Since it looks like they got the mixture screw geometry correct, I guess there's a chance that the needle jet is dimensionally OK, but the brass jet will wear out quickly since the slide needle is constantly buzzing away inside the jet.  The needle jets typically come in .0002" increments (that's two ten-thousandths of an inch), so extremely small changes in the orifice diameter make a significant difference in fuel ratio.  As previously mentioned, you ordered an OEM replacement so that issue should be resolved.  

The enrichment plunger looks OK.  Verify that the rubber seat on the face of the plunger is in good condition, and that it makes up correctly with the metal seat in the carb body.

Your approach to capping off the vacuum nipple on the carb body looks fine to me. Regarding the vent hoses, make sure they are unobstructed, and route them up into the hollow backbone of the frame.

You need to verify that your main air bleed is unobstructed.  If the main air bleed gets plugged with dirt, it will cause a rich condition.  When the needle jet is removed, spray copious amounts of carb cleaner through the main air bleed and make sure the carb cleaner comes out from the needle jet bore in the carb body.

This is the main air bleed.