The prototype is used for final testing of the drivers for the crossover design. It is also used to fine-tune the port size to get the right port tuning. As such, the prototype should be exactly the same as the final design. The wood can be different and some niceties can be avoided but

a) the internal volume must be the same

b) the drivers should be recessed into the front panel so their fronts are flush with the wood

c) the driver positioning in the cabinet should be the same as final

I used a slightly different wood for my prototype (I used a medium density chipboard rather than fiberboard) but otherwise it's the same as the final. Here's a picture of it.

Click the image for a larger version

You can see the port holes on the right. The drivers are all flush-mounted and appropriately screwed into the enclosure. Their positioning agrees with final.

The prototype is used to tune the crossover and to check the port tuning. As a result, I used a bi-wire type of binding post on the back of the enclosure (connectors for the woofers and tweeters are separate). I also used tape to hold the port tubes in the holes so that they could be removed and resized for tuning. Unlike the final, the tubes for the ports are not rounded over at the exit (the side panel) but are left straight. They should be rounded over to reduce port noise at high volume levels, although a 2" diameter port is pretty big for the assume volumes of the speaker.

The other thing I did was to use a solid enclosure partition (no holes for wiring) at first, to check the internal volume of the enclosure and to recheck the V_AS calculations. After doing the checks I drilled a hole to run the wires through.