I have been running a SOA on my YJ for a few years now. Since you are running with a SYE and CV driveshaft, set your axle under your rig with the spring perches and springs roughly in place. Set the rig down carefully onto the axle. Rotate your axle up till the pinion is pointing about 1 deg under a straight line to the t-case output shaft. Tack the perches in place, remove and finish weld. On the front you do the same but set your spring perches at the same angle as the originals were. Your steering geometry is more important than your driveline angles in the front.
As far as gear ratios go, I did not see in your profile whether you are running a 2.5 or a six. With a 4 banger you will most certainly need 4.88 with 35's but 4.56 will work fine on the street with a six. On the trail you may find yourself geared a little high depending on the type of trails you run. I am running and atlas II so low range is fine even with the AX15 and 4.56's and 35" tires. Do the math, but keep in mind the D30 and D35 pinion gear in 4.88's is mighty small. 4.56 pinions ain't nothing worth bragging about though.
'91 YJ, 4.0L 5sp, Atlas II, RE SOA + 2"BDS, 35" Explorer Xterrains, ARB's & 4.56 gears, WARN 9000i