Hi ReelTechnoFreek,
Before you go on, if you're using an AVGA 3000, make sure have these options set like this in mame.ini:
lock_system_modes 0
refresh_dont_care 1
Mortal Kombat games run at 54 Hz, make sure GM is picking the right resolution (look at the Switchres field in the startup screen or create a log). You may need to teak the v-freq/v-hold potentiometer to adjust the monitor to this refresh, this shouldn't be a big issue (50-60 Hz should be in the working range).
Regarding vertical games on horizontal monitor, unless the resulting rotated resolution is equal or below 288 lines, it won't fit in the 15 kHz range, so some compromise will have to be done, usually picking a higher resolution (either 15 kHz-interlaced or 31 kHz when available) and setting bilinear filtering.