Does anyone know the diameter of the stock header pipe on a 2001?

Yes indeed.  That is why I replaced the stock pipe with a 1 3/4" pipe of my own.  It likes it much better...runs happier.

The pipe is 1 3/4" OD, which if I remember correctly leaves about 1 5/8"ID...let me stop and measure it...actual measurement is 1.65".  When checking assorted charts and formula's about header size and length the best middle of the road size seems to be 1 5/8 ID and 33" long +/- 2".  A header of this size, for an engine in the 30-40 hp range, gives peak power at about 4500-5500 rpm.  Those are the numbers I have found while researching this, and on my bike (with a reground cam) the significant power begins coming on at just under 5000 rpm and starts letting off at about 6500...though it will rev easily to 7000 with plenty of power still available.

Keep in mind that there is really good power from idle on up, much more than when the engine was stock.   It is still  amazing to me how well the Savage responds to a carb/exhaust change, literally transforming it with so much more power and responsiveness than compared to stock.
I would be so easy for the factory to do this from the get-go.  And suspension?   Easy to fix...and the factory?  Why don't they do it?  The Savage would sell so much better.
Oh well...there we are.

The exhaust port has been messaged a little, as  posted earlier in the "bike rebuild" in the tech section.  I increased the size of the port by several mm and ended up with a D shaped port...the flat side of the D laying horizontal on the bottom.
The exhaust, from the end of the header, goes up to 2 1/2" OD for about 12" before it enters the 3 1/2" Supertrapp muffler...no discs for baffling at all.  

I ran it with all 12 discs initially but that turned out to be  too restricting so I removed them all except for a few to mount the reverse cone end piece, which has a 2" opening...so no restricting effect from the few discs...they are just a mounting base for the cone........looks good and sounds good.