The problem you will hit Doog is if you use two 18mm pieces of MDF (36mm body) your mock route wont be deep enough to house the pups, switch and pots. Bare in mind a standard mono jack is about 25mm deep.
If you use an angled 3-way switch (like Jazzmaster) you will get away with a shallow route but they are expensive compared to the standard Epiphone 3-way. Mini alpha pots may gain you some some space as will cutting off height adjustment screws on the pickups to minimum (although some companies drill an extended hole for these).
With the neck pocket route you should just get away with it, even if it means raising the bridge a little. My Franrite neck pocket is only about 18mm deep.
You can get 25mm MDF (50mm body) but its going to make it a heavy guitar and a 'swimming pool' route will be essential to lose some weight.
I think MDF is the best choice with manmade board, Plywood is difficult to finish on the edge. BC Rich used ply when the company went to shit in the late 80's and even through thick paint you can see the lines in the plywood.
Hope that helps. Look forward to seeing the progress and any probs give us a shout mate