From what I understand, the owners/admins of Christian forums did a majority of their coding in house. Regardless, you can pull some of the side bar results by searching here for left and right column hacks and/or take a look at vBadvanced.
Layout can be achieved by modifying your Depth of Forums in your Forum Listings Display Options. However theirs appears to be quite modified so it's much more involved that just changing a few options.
Google ads under category strips. I'm sure there's a modification for it somewhere on here... Try searching the mod section.
lol I guess in a nutshell, you will not find a step by step. Try to find a similar style and modify from there.