You have to pass through immigration in KL so you “enter” Malaysia. You then have to check-in to your return flight and go back through immigration to “exit” Malaysia.
You cannot wait in the transit area because you must have the enter/exit stamps from immigration.
Triple check every part of your name and passport details. So many times the “auto scan” of the passport gets things wrong. Instant rejection if any details are wrong.
Best to get a new passport. An extension would be issued for one year or until the expiry of the passport. So if you were applying in March or April it would only be valid until September and you’d have to apply again for a year one using the new passport.
Join a Facebook group “UK Visa Information Thailand”
People with prior experience can help you there. From what I gather it’s difficult to obtain unless your GF has strong ties to Thailand and therefore proves she’d be coming back.