Since those consulates in Malaysia went to the eVisa online system they sure aren't know for speedy processing (like they used to be when you walked up to them)
I would say you could get the 90 day Non-O visa from Kuala Lumpur, Penang or Kota Bharu, but I'd plan on being their the processing time they post on their website (which you would have to look at for the one you select)
Shouldn't have much trouble other than the processing time. The system is straight foward, GO to malaysia, select the consulate based on where you're staying there, log in, upload proof you're in Malaysia (visa/entry stamp) upload the documentation, proof of funds, submit the application and pay online. Then you wait for them to email you as far as if it's approved or rejected.
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