Not sure if I can help, but I will try.
How I did it was to take a large peice of cardboard (maybe 20 x 30 iinches) and hold it against where I wanted the console to flush up to. I had to trim that about 6 or 8 times to get it right. Use a pen to mark what you want to cut. Once I had it where I liked it, I laid it up against the MDF and used it as a template to mark my cut on the MDF.
In my CrownVic I removed the cupholder/ashtray. This gives you the space to work AND allows you to "Lock" the console into the rails that the cupholder/ashtray uses. You can add a few small notches where the console touches the dash to make it hold much better.
If you like, I can post a few more pics of mine and focus on the area where dash meets console?
Hope that helps. Let me know if you want pics.