It's not very clear if you are reporting one problem or two. Assuming you are reporting two problems:
1) Why the "Gates connect to door 2L" is considered to be a problem ? And which gates are you referring to ?
Assuming you mean "jetways", if they are standard jetways, the are controlled ONLY by the airplane OWN Airplane.cfg, totally unrelated with GSX. If they are SODE jetways, you can *CHOOSE* which jetway to use, of course only from those that can connect to doors, depending on your parking position. If you have enabled the Automatic Services option in GSX, they will connect to the airplane PREFERRED EXIT. Assuming, of course, they can.
2) The 2nd problem is a known issue, which we'll try to fix in a future update, that happens when two different stairs models are called a the same time, for the 1st and 2nd door.