I recently installed an SE Heavy Breather. While I was at work today my father in law tinkered in the bike some. Bike would idle fine with choke pushed in but once it drops into gear it wants to stall out. Is there an air/fuel mixture screw to solve this or does something else need done? Thanks.

 

U might be EFI (fuel injected) and need a tuner to correct the A/F ratio.

 

Its running lean, you probably need to have it rejetted.

 

OP mentioned choke, havn't seen a FI with one yet.

 

I believe Sportsters went FI in 2007 so if you have carb, you may want to reset your idle mixture screw and idle speed as well as your accelerator pump. However, be sure to check for intake and exhaust leaks first, especially leaks at the manifold..

 

When the choke it left partially out then the bike runs fine. Can it be rode like that? Anywhere I can adjust to give the bike more air without rejet?

 

You can fix it with a band aid, or do it right. You may get by with the choke partially engaged, or you may fowl your plugs.

 

Will it hurt the bike to ride like that?

 

Yes. too much unburned gas in the cylinders, gets into the oil, thins it, shortens engine life.

 

You can change your pipes. You can install a heavy breather. However, you can NOT do both, without re-jetting the carb.
Here's a Harley Certified, Master Technician, that knows Jack. Fast talking, but there's info buried in his dialog for Sportsters ("XL"). The video discusses a big-twin. Don't let that confuse you.
Removing the plug that covers the air/fuel mixture screw, begins around 7:38. Watch the entire video. The plug covering the mixture screw, was a quick-fix to satisfy the EPA, decades ago. Mother Harley caught on and made it easy to remedy. Then, fuel infection came into play. Two dollars for a jet, verses $400 for a tuner. I love carburetors.
You want a jet from a 90's era 1200 Sportster. I don't remember the part #. Too many beers ago.
I bet you'll have more questions. It's an easy procedure, once you've done it, and he makes it look super easy working in his shop. Actually, if you know what you're doing, the plug covering the mixture screw can be be removed without taking the carb off the intake. You'll probably wanna remove the carb. Put a new boot on the intake while you're at it. After 13 years, your '06 may be dry rotted/cracked and creating an air leak.
Also, it's not a "choke". It's an enrichner. It doesn't reduce air, it increases fuel.