Well I have been using a similar concept to what your thinking, only I've been leaving the keyboard in one peice, just mounting it behind a panel. I use one for combat sims, and one for FS
As for the usb thing, I got a ps2 to usb adapter for about $20 that way you can use a cheap and simple (old)keyboard, which are getting hard to find(new)

Drill and glue is pretty much exactly how I did this, attached is a sectional of how I made the flap switch(and trim wheel/pivot)



I dont really have any instructions but this is a picture of where I started....I made the base and stood up the keyboard which gave me a chance to use stickers as labels and plan out the mapping of the buttons

It is only a matter of time before I redo both of these projects and incorporate some actual switches and dials, even a dedicated gauges monitor.....but until life stops getting in the damn way these little units make my simming a little more........fun
I got the original idea from this http://rogerdodger.net/diyflightsims.html

The front peice of 1/8" painted MDF is close to the keyboard but not touching it. The buttons on the FS panel were made with 3/4" MDF stock milled down to 3/4"x 3/4" x 3/4" cubes then painted......on my second panel (combat sim panel)I used 1/2" doweling and cut it down into 3/4" pieces then painted them, this was a much easier solution, and it made the holes in the front panel MUCH easier (5/8" drill)

I would definately suggest dowels. I used silicon to attach the buttons to the keyboard buttons. the keyboard buttons are 3/4" so you can use them side by side

The two buttons above the nav com buttons are the stock zoom + -, they also work (sometimes) to increase or decrease the selected nav or com frequency which are right below them. As you can see on my prototype version I was hoping to be able to adjust alt hold settings  , and for that matter speed hold settings, these were just wishfull thinking and they never made the final cut......this was exactly the reason I showed you that picture, make sure you do something similar before you start making final plans because you have the option to completely relayout the button assignments and this takes a bit of trial and error.
If you dont mind me asking......what are you planning 

Hey Rom, thanks again I am still in the designing phase LOL, But I will for sure post a pic when I get the layout done to get your input on what I should change, remove, add etc...

Nice the see the yoke there.

best,

.............john