Hey guys,
I have a 2006 Savage with about 10200 miles on it that I've been riding for a couple of weeks.  Two strange things just happened and I'm not sure if they're related, so I was hoping to get some advice from the experts.  

1) After about 45 minutes of stop and go riding, it got really difficult to shift into higher gears, especially going from first to second.  Instead of just moving my foot, I have to jerk or kick the lever up to shift.  No issues when the bike is cold, but this has happened twice after taking the bike on longer runs.

2) About 1/2 hour after #1 happened, I was stopped at a light on a steep hill and I stalled the engine while trying to get the bike going (noob moment  ).  But I got the bike started again and got going right away.

About 10 minutes later though, while stopped at another light on flat ground, the bike felt like it was slowly losing revs.  I gave it a little more gas with the clutch pulled in (not moving), but the bike slowly just died.  I thought maybe I had run out of gas, so I switched to reserve and started the bike again.  Once I got rolling, the bike wouldn't shift into second gear so I pulled into a parking lot and turned off the bike.

Oil levels were fine, gas was fine, but I let the bike sit for about 5 minutes and just shifted gears with the bike off.  Then I started the bike again and drove 10 minutes home and stopped about 6 stops signs with no issues at all.

What is going on here?  Are these two problems related?

Thanks for your help!

????? That is some strange goings on... ...
May be two problems...

Do this test... for the bogging and dieing...
Test your Petcock,.. don't just turn it to Prime..

... other might be clutch or shifting...
Is your shift rod bent?... (from shift lever to tranny case?...
What oil are you using?.. (not "fuel saving" car oil)...
Is the clutch cable scratchy or stiff?... (Need lube, or frayed inside)...

... or... desperate times... bad clutch... (but I wouldn't expect that to be intermittent... and shifting in higher gears should be easier.  They should be easy without a clutch at all)...
... or real trouble... shift dogs on the fritz...

The clutch can affect shifting, but not the engine running.  If your clutch were hydraulic, I might suspect a leak somewhere, but it's a cabled clutch on the Savage.   Do you have the proper play with the clutch released (about 1/2 inch a the end of the lever)?   Also make sure the adjustment nuts are not loose.

BTW, 1st and 2nd are LOWER gears, not HIGHER gears; the sequence is starting with low gear and shifting toward higher gears.  Also JOG is right, it will be harder to shift the lower gears in clutchless mode.   When clutchless shifting, try to reduce pressure on the gears by synchronizing the throttle to the speed of the bike in the particular gear you're in.    In other words, heavy acceleration or deceleration will make the gears harder to shift.   It takes finesse and experience, but it helps shifting sans clutch.

yes

Yea, that was waay too much slack, It has to have some slack, but not that much,

I have the similar problem on a 2012 with 900miles. When it is cold it shifts as I think it should with no problems. When it is fully warmed up
it really clunks from 2nd to 3rd and when stopping it can be hard to go to 1st. I need to let the clutch out slighly to make it go into 1st. I just checked the case markings fo the end of the clutch arm, right in the middle. The cable slack is only enough that when I wiggle the clutch arm I get a ticking at the hand lever. Probably less than a half inch at the end of the hand lever. Is it that the oil is thinning or that the fit of the gear set is tightening due to heat? Standard oil and filter when new. 10w40 Valvoline motorcycle oil and filter at 110miles. Dealer oil and filter at 600 miles. I am gouing to switch to Mobil1 4T and a filter pretty soon to see if the synthetic helps. I hope it wears in by 3000 miles. Any additional ideas why it changes from cold to fully warm?