Hey guys. Got the 2009 S40 put back together this weekend with the basic mods done. According to Google I'm 1,500 feet above sea level. Here's a quick list of what I did:

(1) LANCER JetSet kit - #150 main jet, #50 pilot, 3 washers on the needle
(2) K&N air filter, stock airbox
(3) Harley Dyna muffler
(4) Idle Mix Screw backed out 1.5 turns, currently.
(5) NGK Iridium spark plug
(6) Raptor 660 petcock (genuine Yamaha part)

The good: when she's up and running, there's a noticeable increase in power and smoothness all the way up to 4th gear - haven't had time to get in a stretch where I can hit 5th so not sure about that.

The bad: 1st maiden voyage yesterday after the mods, there was a lot of popping and cracking between each gear change, and a nice big bang when I shut it off. I pulled the choke all the way out this morning, and hit the starter once, nothing. Second try, it started to lope really slow but still shut off when I let off the starter. Third time, I hit the starter and when it got to the slow lope I turned the throttle a bit and it took right off. Second ride around the neighborhood, the pops and cracks between gear shifts was gone but still got a pop when I shut her down.

Any thoughts on how to cure the hard starting and backfire on shutdown? Thanks in advance!

ok Batman, I'm gonna try three turns out first and see what happens. Thanks!

That's so strange I'd be pulling the carb and looking to find out why, or at least adjusting the screw with the bike running to see if the motor speed changes(it should) .Be sure to slow the idle speed down using the idle speed screw on the left side of the carb before you do so that you can hear the motor change speed.          
      If you pull the carb I'd look very closely at the pilot jet to make sure it's tight ,and I'd make sure your float level is set to the correct level,  for starters. I f you pulled all the jets from the carb ,top and bottom make sure you didn't swap the air jet and the main jet on reassembly.
       When you screw the fuel screw in all the way you may not stall the bike as there are two channels that the fuel uses to enter the carb and the screw only blocks one,(fine tunes it) but you should have at least heard it slow down. I might believe that it would run if you had gone to a larger pilot jet like a 55 or 60 ,but you went smaller so I doubt it , something's fishy.  You can't properly adjust the fuel screw if the motor isn't warmed up and running.
   You had better take a look at the spacer mod again also ,if you placed the washers on the needle jet incorrectly you may have lowered rather than raised the needle , and have raised the slide with the idle screw to over compensate (provide enough fuel even at idle to make the idle circuit unneeded) which may be why you can close the fuel screw and it still runs,and if you open it ,it becomes too rich. If you don't have a Clymer book ,you can go to a site like Ron Ayers for an expanded view of the carb.
               Good luck!
     

The vacuum port being open would cause the bike to run very lean at idle when the vacuum is at it's highest, his problem is just the opposite ,he's running rich. It has to be a fuel problem ,and it's inside the carb. the only other thing I can think of that may be amiss is that the float could leak or the float valve could be leaking by or the O-ring around the float valve seat could be old/ damaged. that might cause the bowl level to run higher and send to much fuel into the carb.

BTW I'm pretty sure mine had a 145 main jet and a 47.5 pilot jet when I took it down.

Batman, just got the old parts out and checked, I DID have a 52.5 pilot and a 145 man jet to start with.  I'll put the 52.5 back in and see what happens.

Big Al, I don't think that will solve your problem ,but I think you should run that 52.5 jet. I would suggest you revisit the spacer mod, check that the washers are positioned right, that when you look inside the barrel of the slide you can see light through the two tiny holles in the bottom of it(vacuum ports) and that the brass plate ,which has a small dimple very near the jet needle ,is installed with the dimple protruding downward . and check that the air jet from the top wasn't switched with the main jet, also that there is a washer between the main jet and the body of the needle jet (it holds it up in place in the carb body) if it's not there ,the jet (the cylinder with the hole ) can fall down away from the carb body,  and lots of extra unmetered fuel will pass around it ) which could also be your problem.