Hey guys! Hoping to get some help with my bike, I'm at a little bit of a lost.
I have a 2012 savage, with about 13,000 miles. I purchased it last year from a guy who commuted every day on it (hence the high miles), he kept really god care of it and it ran great for a while. About 4 months ago I started having this weird, choking like problem. I've not been riding long, so I apologize if my language isn't apt! I've read and searched through other threads on the forum, but couldn't find something that quite matched my issue.
The issue comes during riding. The bike would start up fine, I'd ride it for a couple miles, sometimes more sometimes much less, than it would start juddering, and losing. Naturally I thought it was a gas thing the first time, but having ridden it lots with a full tank, the same issue occurs. I had to get it towed to a shop after one ride, I got less than a mile, and it started sputtering and chugging, I gave it a lot of throttle, that usually helped keep it going, but as soon as I would ease of the gas, the bike would just cut out and die. The mechanic changed the jetting and altered the gas/air mixture, which he tested and said worked fine. I took it for a ride, and within a couple miles the same issue was happening, I came to a stop at a light and the bike just died, it struggled to start again, the starter just turning, eventually with a lot of gas it would roar into life, but I still has to rid in low gears, with the throttle almost wide open to prevent it from dying. The mechanic said at he thinks it's potentially electric, but has no real knowledge of these bikes and doesn't want to just replace something. Some help and info on this situation would be incredible, I'm riding my wife's Vespa and missing my thumper! I changed the oil about 6/7 months ago, riding less than a 100 miles since the change, I also changed out the air filter for a new one. Hope that helps. Appreciate your help in advance!

if you have the stock petcock, it most likely needs changing to a raptor.  Have you read about that on here yet?

Or....the petcock diaphragm could have a hole in it, and is allowing fuel to flow down the vacuum line and creating a mixture that is too rich.  The bike would start and run when cold......but progressively run worse as the engine warms up (also run worse at low throttle settings).

As others have stated....it sure sound like a failure of the stock petcock to me.  To find out, remove the vacuum line and see if there is any fuel in it (small black line with the spring on the outside of it that connects to the right side of the carb).  If there is any fuel in the line that is an indication the diaphragm has a leak in it.  Shove a golf tee in the vacuum line, then plug the port on the side of the carb with a rubber cap (or another piece of hose and a golf tee, set the petcock on PRIME....and see if the problems are gone.

If the bike runs OK with the vacuum line disconnected, the vacuum port on the carb plugged, and the petcock on PRIME....it is time for you to order your genuine Yamaha Raptor petcock (accept no Chinese substitutes).  Only use a genuine Yamaha  5LP-24500-01-00

Dave wrote on 09/01/15 at 13:56:56:

Or....the petcock diaphragm could have a hole in it, and is allowing fuel to flow down the vacuum line and creating a mixture that is too rich.  The bike would start and run when cold......but progressively run worse as the engine warms up (also run worse at low throttle settings).

As others have stated....it sure sound like a failure of the stock petcock to me.  To find out, remove the vacuum line and see if there is any fuel in it (small black line with the spring on the outside of it that connects to the right side of the carb).  If there is any fuel in the line that is an indication the diaphragm has a leak in it.  Shove a golf tee in the vacuum line, then plug the port on the side of the carb with a rubber cap (or another piece of hose and a golf tee, set the petcock on PRIME....and see if the problems are gone.

If the bike runs OK with the vacuum line disconnected, the vacuum port on the carb plugged, and the petcock on PRIME....it is time for you to order your genuine Yamaha Raptor petcock (accept no Chinese substitutes).  Only use a genuine Yamaha  5LP-24500-01-00

This might be the issue! I'll have to try and see if that works, I'm away from the bike, but will make some time to try this out over the next few days.

The, Raptor, (Real one), Petcock change, is not money wasted.
And the more, ‘ethanol’, gas run through the, ‘factory one’, the faster it will fail.
And while you are their, do a, ‘fuel’, in line filter add.
Again, not money wasted, and both cheep, to do.
Filter: http://suzukisavage.com/cgi-bin/YaBB.pl?num=1211846392
Just maybe, you got some, ‘chunks’ in the tank, that is restricting the flow.

This link, is your friend, for DYI’ing.
http://suzukisavage.com/cgi-bin/YaBB.pl?num=1181745927
And, DYI,
If you go to a Dealer, you will be shelling outs TONS on money, you don’t have to.

( Well, unless you are like a certain Moderator of this site, who LOVES to give his money away)

If the Raptor & Filter, don’t solve the problem,
then ask again.
The Cumulative knowledge here, on this site, about the LS640/S40 ICE, is Legendary.

I have played with small, 3-15 HP Single, ICE’s (Internal Combustion Engines),
for probably 40 years.
NEVER, did I think that a,  ’06, S40, was to be treated like a,
Pre, Lead, Pre Ethanol, gas. Pre, Zinc in the oil, ICE.

If you like, ’tinkering’, you will LOVE this MC.
If you don’t, then sell it,
and buy something you will take to the, ‘dealer’ every year,
and also hand him several hundred dollars, to keep running.

santacruzsavage wrote on 09/01/15 at 14:00:27:

I have read about it, the first time I thought i had an issue, I took it into the shop and the mechanic told me it was the petcock and he just flushed the fuel lines. We didn't replace the petcock, so it could potentially be that, would that effect how well the fuel is getting to the engine/carb?

Sadly, this does sound like a typical dealer response. "I see your problem but this is what the manual says to do...I know nothing beyond that"

Get a Raptor fuel valve and enjoy you bike. It's a 10 minute fix.

My earlier post , you know, where I said
Save the hassles, put a petcock on...
The part about the cam chain tensioner is really important. I hope you go back and read it again.

interesting. this sounds a lot like my problem.

raptor petcock you say eh? i'll look into that.....
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looked into this petcock and realized i think i already have this.  while reading about it i remember the guy i got my savage from telling me something about a quad part that was used.  i thought it was a choke but this makes way more sense..... i still think i'll get a new one though it might have some issues..