Hello All-

I'm a noob and a Savage fan here in upstate NY posting for the first time. Been riding for about a year. Initially on a Honda Cm400 that died (long story). So, now I'm riding the LS650 I bought a few months ago from someone who had it a little while and claimed no issues and up til now it has been fine.

Been reading this site ALOT, but I've hit a wall and wondering how to proceed.

What I have:
1999 LS650P
Raptor Petcock
11,000 miles
3rd owner.

Ran very well when I got it and had no issues except for some sputter or "tug"-like feeling around 60-65mph. Came and went and I don't mind since the speed limit around here pretty much maxes out at 55 and I'm too green for highways.

What I did:
Tried to upgrade to the dyna muffler the previous owner threw in with the sale.
Went on well enough, but got some backfire and low end sputter. So, in researching here I tried a few of the suggested mods to work it out.

It now has:
2/3rd white spacer
55 pilot (up from the 52.5)
152.5 Main (up from the 145)
(Also tested out a 150 Main)

Getting a lot of sputter and backfire.
I tried different jet combos and the final one above worked best initially, but started sputtering and backfiring really bad after about an hour.
I put in fresh gas, I changed the air filter, the header bolts are tight, I put in a new header gasket and theres no leaks I can tell from the exhaust. I cleaned out the carb during the first rejet attempt,  its clean to the best of my knowledge and as I said before it was running well before I changed the muffler.
I know you've all found a way to make different mufflers work and since the Dyna is the most common I figured I wasn't going out on a limb too far as my first mod attempt.
The brass plug on the carb was already pulled by someone in the past and I've tried following the tuning advice. The idle is nice and high but the A/F mix screw doesn't seem to be having much effect no matter how I turn it.
Again, I'm new and my senses are not as knowledgeable as some of yours. I'm pretty comfortable mechanically, but just wondering if this is a matter of tuning and reconfiguring my jets or if I'm searching in the wrong place? Not double checking the right thing Or should I dial it all back and start over....?  
Thanks in advance to anyone out there that has some words of wisdom. You've all been a big help in my learning experience so far and its been fun -frustrating, but that can be fun too.

I will also wait for the more expert tuners to chime in but wanted to mention that at 11K miles you are due to inspect (and probably change) the cam chain tensioner.

With no intake mod you could run the 52.5 pilot jet, I would use the 152.5 main jet with the PMS screw out three turns

They spit, sputter, backfire and fart when the slide gets stuck.  The throttle plate opens and the slide doesn't, you get a really lean condition.  I had this problem and noticed the black coating on the slide was rubbing off and building up inside the carb.  Also, a touch of grease around the top of the diaphragm doesn't hurt.  Oh and make sure it's seated correctly.

Wow. Thanks for all the feedback guys, very much appreciated and these are very useful tips that I'll be using.
•The elevation for my town says 960ft ASL. if that helps any.

And it's true what Batman said, it changes drastically over very short distances. So that will be its own challenge. I believe I read a few of batmans posts along the way since I saw you were upstate as well and running a Dyna. I'll try the stock pilot and 150 again since it seems real hungry for gas as it is now.

The vacuum port is plugged with a crimped hose, unless anyone has a suggestion for a better seal - i'm open to ideas.
I will check the baffle on the muffler just to be sure as I don't believe I  inspected it as closely as I should have. I also bought a Ryca connector just to make sure the connection is solid.

I did notice the slide was scuffed when I changed the white spacer. Is there a way to lube it or safely clean it?
I'll look into that Oldfeller filter. Any intake tests worth trying? I know some have tried running it with the filter door off to check intake need.

I'll try a few more turns out on the PMS as my next step, Yoshi. thanks.
Right now I believe it's at 2.

I've been concerned about the cam chain, Tocsik and once this is worked out (if) then I'll have a look at it this winter once I have some cold weather time to do some inspecting.

Thanks again everyone.

Tocsik - thanks, I will definitely get some!

Tocsik  and Stewwells  are right on ! As for being at 960 ft, I'm at 850 ,but ride the thruway( 450) or up in the mts( 2000-2500 ) and never miss a beat. at lower elevations you'll run a bit leaner ,but a 150 is two sizes up from the stock 145 , so you won't be lean enough to hurt the motor(run hot) , at higher elevation you'll run a bit rich ,which won't damage at all.

So, for those that may read this I have good news!  Finally had success working things out and very happy with the results.
Ended up dialing things back to the beginning and retracing my steps. I put three washers in the needle spacer to get it back to stock condition. Then did some maintenance such as charging up the battery and cleaning out the carb (again) and replacing some possibly worn out o-rings - plus putting a new stock size pilot jet in (the one in there looked scratched and the screw slot was chewed up) but kept the 150 Main. I found a nice chunk of who-knows-what stuck in the float needle screen, so it was certainly worth the extra careful inspection.
I cleaned out the air box gunk and made an Oldfeller style air filter.
The main culprit i think was the header gasket that I felt didn't quite sit right the first time around. I put in a new one and carefully, slowly tightened the header exhaust clamp. I got some new clamps for all the hose connections and even put in a fresh fuel line hose with fuel filter. The moment of truth came when she fired up strong and clean and there was no waver or hesitation in the idle. I let it warm up for a full 20mins then gave her a go on the road and...ZOOM! The throttle response was amazing and there were no pops, no stutters, sputters or backfires - just a perfect little crackle on decel that I like Alot!. I couldnt stop riding around for hours... All in all, I can't really pinpoint what was wrong earlier but it all clicked into place with a lot of patience, research and help from this forum. Could not have done it without this source of community and information.
Ride safe yall!