"i was wondering if it makes any differece using 5/8 or 3/4 MDF?"
Seems to be personal preference. If you are working off of dimensioned plans, some of the dimensions may have to be changed if the plans were layed out for one or the other.
"For the control panel how do i make the holes for the joystick and buttons laid out evenly?"
I laid mine out in autocad, then plotted it lifesize. Taped the layout to my CP and punched center holes. Theres templates out there - I'm just not sure where to search off the top of my head.
Also does anyoen know a tutorial that has step by step on making a cabinet.
Google "mame cabinet plans", thats how I found mine. Lots of folks have based their cabs on Lusid's drawings - its a great place to start.
Still kinda a newb myself - but learning quick. Misteaks

are a great way to learn.