How did you release the tensioner onto the chain? YOu didnt press it out to make it tight, did you? Did you take the chain off?

If it still pulls right & starts up right once its warmed up, I have a hard time seein a timing issue,, Im kida stumped,., lets let some of the Deep Innards guys have a shot at it.

Did you block off the vacuum tap on the carb?...

Yes, the vacuum is blocked off. And yes I had it up to 55-60, accelerated pretty hard, ran steady at 55, and it pulled OK through the gears, but the seat of my pants said it could be better. No missing or noticeable dead spots.  I didn't hear any loud ticking or ratttling at high speed (at least not through my helmet).  It is mainly when it is idling and when I roll the throttle on a little in neutral that I can hear a bit of noise I hadn't heard before. It doesn't seem to get louder or related to the speed of the engine that I can tell.  I may need to ride it around without my helmet and give it a listen. I could just be paranoid about the engine noises, but again, it's the hard starting and smoking that has me baffled.

No, didn't adjust the valves after doing the work. I thought about that, but didn't think the stuff I did would affect the valve adjustment. Might not be a bad idea to just do it.  The stuff on other forums for other bikes seem to indicated oil leaking past the valve guides overnight. I just think it is kinda weird that didn't happen before the work I did.

If he had a bad vac petcock it could have been supplying extra fuel through alternate pathways.

Change to a Raptor, no extra fuel any more.  

Think about him having starting/idling characteristics that are now apparent when before they were being masked by vac petcock malfunctions.

Afer all "poor starting" that requires a choke in wintertime is NORMAL for most folks.    Quick starting fluid being needed, not so much.

(see comments below on bad gas)

=========================

Smoking at start up, ask for mileage and oil type used.

Before I tore an engine down for Smoking at start up, I'd put in AN APPROPRIATE AMOUNT of a seal sweller into the oil and run it for an oil change to see if anything changes.   Remember, you will only use 20-25% of what is recommended for a CAR (on most bottles, anyway).

This treatment does change the weepage amount around the valve seals enough to let you see the change and let you know where your internal oil drips are coming from IF it is the valve seal.  

Once again, excess fuel can cause smoking at start up too.  

(see petcock off-on drill below)


=================


That steady whirrrr noise from the cam chain sprocket area is puzzlesome to me -- our cam chain system is by and large silent unless it has run completely out of adjuster range.

Agreed that step #1 is to do a full valve adjustment and report back what the existing clearance numbers really were before you fixed them.


====================


Next, always shut your petcock OFF as soon as you get off the bike and when you get ready to go, start it first then get it idling good then turn your petcock ON.

When you report back on the effects if any from this little trick you will be telling us if your float valve and seat are leaking on you some.


========================


You would be amazed at how many odd things take place after a rebuild because you had a very old partial tank of gas that you had topped off with whatever you had sitting around in a can somewhere.

Get some fresh gas in the bike too ....

S-P
Did your petcock malfunction and did you get fuel in your airbox? in your crankcase?
Did you run the bike with fuel in the oil? (might not have noticed it at the time)
When you had your case side off, did you cover it so as not to get moisture in the case? (could be residual water slipping past the piston rings and burning)
Just asking.... i'm not a savage guru... so i'll let them talk ya thru it.