Best thing to do is to to go find yourself a pile o' rocks some place and flex out your suspension, see what kind of length you'll need when you're fully extended, then fully compressed. You want a shock that will be handle both situations, with a little bit of wiggle-room. Bumpstops and shock limiting straps can be used to minimize overcompressing or over-extending shocks.
Shocks have the most dampening effect when they're mounted straight up and down. I think at a 30 deg. angle that you still get around 86% dampening efficiency- so, you can mount them at an angle to run longer shocks, and still get reasonable dampening.
I just put the ford shock towers on my fj40, used lower shock mounts from Ruffstuff specialties on the axle (I used shock mounts from Spidertrax for the rear).
Here's a good write-up for installing the Ford shock towers:
http://www.in2jeep.com/fordshockmt.htm
Hope that helps!