I blew out the cross over on my stock pipes on my 2002 xl1200. I was given a set of 2" drag pipes. Is there any carb. adj I need to do to keep from damaging my bike?

A few things come to mind.

I'm not familiar with the Mallory ignition system, but does it have an adjustable Rev limiter?
Is it set too low (like 3000 RPMs)?

Is the carb set up right?
Here's S&S's tuning instructions for a Shorty "E" or "G" carb (you didn't state what model of S&S carb you're running):

http://www.sscycle.com/tech-info/carb-quick-guide/

Finally, here's S&S's take on straight pipes:

"Open drag pipes work reasonably well for peak horsepower numbers on some engines but limit low speed performance on the street and can be nearly impossible to carburet."
"Overall, drag pipes are a poor choice for street use. Drag pipes offer nothing to break up the reversion wave pulse. This wave goes down the pipe and then the wave returns back up the pipes. When this wave is in proper time sync to hit the exhaust valve when it is open (pipe length affects the rpm that this happens) it allows the wave to enter the cylinder and when the intake is open during cam overlap it travels across the top of the piston (it is near top of the cylinder at this time) and out the intake valve. This wave continues out the intake through the carb where the next intake stroke draws it all in again. Each time this wave passes through the carburetor the venturi adds gas and makes the next incoming charge richer creating a flat spot or stumble or worse a blubber at this rpm. The longer the duration cam the worse this situation is. Also larger diameter drag pipes and fishtails seem to make this situation worse."

Gently turn the needle valves in till they stop. Then turn eachvalve one full turn out.

first try cleaning the carbs, new spark plugs and adjust valve clearances, new oil and clean air filter, before any screw adjustments, which will need some vacumn gauges attached to set the carb sync

That is sometimes caused by leaking exhaust valves or air getting in to the intake manifold.

you need to put the stock jets back in, be very carefull not to nick anything in there

FIRST, YOU DIDN'T NEED TO REJET THE CARBS. I WOULD PUT THE STOCK JETS BACK IN IT WILL RUN JUST FINE. YOU NEED TO HAVE IT RUN ON AN EGA MACHINE TO TUNE IT PROPERLY.

could be 2 different things,#1 could be the carb that needs cleaned and adjusted( i would try that first,easy.)....#2 valves need adjusted ( is the exhaust pipe getting red hot where it comes off engine?) the factory settings for the valve clearance is 0.04 for intake and exhaust both (with stock carb and head)

your factory jets should be ok with stock carb and exhaust,unless it came from way down south or someone changed them.factory jets are main jet #380,pilot jet #30

I also have a 1985 Cr125 with the aftermarket DG pipe. The ATAC chamber needs to be removed to install this pipe.

set you carb adjustments at 1 1/4 and try that