Check out forum member boywonder's build-thread postings on these two pages in particular, where he has a great set of photos and write-up for upgrading the hardware on the penthouse mechanism. You'll have to scroll down a bit on each page to see the specific postings that speak to and picture the penthouse hardware.
http://www.sportsmobileforum.com/for...p-10808-3.html
and
http://www.sportsmobileforum.com/for...p-10808-6.html
Looks like he calls out a length of 2 1/2".
**OF NOTE:
When he replaced his bolts, he decided to increase their thickness slightly.
(Originals were 1/4 - 20.....but he ended up drilling out his holes a bit bigger and going with a shoulder bolt of spec 5/16" x 2 1/2" long.)
PS: I see you have a Dodge SMB, I'm assuming the bolts are the same specs for your penthouse hardware as they would be in a Ford-based rig...but someone else should probably confirm this.