Sounds like a plan. You basically measure 90 degree from your lower arms right?
Yup... at ride height. Just mock up your lower shock mount on the axle. The semi-hard part is determining the height of the tower. You need to think long and hard about your shock and if you are happy with their compressed and extended length. Don't get greedy and think you can have to much in either direction because you'll either be into your tub, or unseating your spring. If you're using a 10' travel shock... I'd go 5 up and 5 down. This makes the cut critical if you're using a tapered shock tower because obviously it's height determines the size of the notch in the frame.
Before you finish weld anything cycle the suspension, full, bump, full droop and full flex both ways at ride height with the rear springs out.
So the towers are angled right for needed shock clearance through the entire suspension travel. Remember Nate has long arms makes the axle move less front to back than short arms.
My Tinkering and wheeling thread http://tinyurl.com/pbwdm5u
I prefer to use full, hard bump as the determinant of the position of the shock mounts. Set the axle as high as it can possibly go and adjust the bump stops to stop it just before the first point of interference--remember, the foam insert will completely compress so leave it out of the equation.
Since the position of the upper and lower shock mounts are floating (you're free to put them wherever you want) the only thing that matters is the distance between them at full bump. Use zip ties to keep the shock compressed 1/2" before completely bottoming out--the eye-eye measurement is the distance you need to set the upper and lower mount bolt holes apart from each other with the axle at full bump. Roughly determine where the lower mount is gonna go (just deal with one side right now) and tack it there....make sure it's easy to remove and only tacked on strong enough to hold the shock. It's likely you'll need to adjust it laterally before you burn it home.
Bolt up the shock and make sure you can fit the tower in the space required at the height it needs to be at. Only cut the frame once you've firmly established that you're happy with the location of the mount, especially if the tower is tapered. When going through the process, work through it slowly and methodically. Common sense goes a long way here....don't overcomplicate it and it'll all go well. If you're considering running longer and/or a different shock in the future, acquire the extended/compressed lengths and use those to setup your mounts instead of your current shocks. I would also consider mounting the towers up as high as possible and just setting the position of the lower mounts to agree with your shock travel and up/down bias....once the tower is burned in, it's in. The lower mounts are much easier to cut off and move/replace in the future if you do end up switching to a different length shock.
Hopefully that all makes sense. My best advice--set everything up at full bump and let ride height be what it will be. Full bump is what matters.