I looked at the plans and if you notice the panel(Panel B x 1) to the right of the sub baffle is the same but with no hole for the sub. The baffles are pretty much square so the measurements should be the same.
As for the bottom ports you will need nothing. You might want to round off the inside and outside edges of each port to reduce turbulence(aka. port fart).
I have used this with good success(top port)but it is a little shorter than the original length that is suggested.
http://www.parts-express.com/pe/showdetl.cfm?Partnumber=260-401If you go back thru the HWK post you will find some people modded the original design. I know, I am one of them. I would build it to specs first then if you are not happy you can change it to the way you like. Just my two cents. Let me know if you need more info.
HT-EXT