That your rear DS is an aftermarket CV driveshaft is not why you had u-joints go bad. What can cause u-joints to go bad is if the rear pinion angle is incorrect which causes the u-joints to vibrate which will ruin them in short order. Or lack of lubrication from being old if they are sealed, or lack of lubrication if they have grease fittiings on them and they aren't greased regularly. Personally I run sealed u-joints in my driveshafts and prefer them over greasable u-joints for the type of wheeling I do.
Yes it's a very good thing to have a CV driveshaft and a SYE installed which is pretty much required once you have a suspension lift that is taller than 4" as your 6" is. The SYE shortens the transfer case length which allows for a longer driveshaft which decreases its operating angle which decreases the angle at the u-joints which is a good thing.
With a two u-joint driveshaft, like the factory installs in the rear , the two u-joints divide the angle as you see below in the first illustration. The problem is that that angle gets very steep with a tall suspension lift and the u-joints can't cope with such steep angles so they vibrate with tall suspension lifts.
With a three u-joint (CV) driveshaft as shown in the second illustration below, the rear u-joint sees no angle at all. At the front CV joint, the two u-joints divide the angle between them so neither u-joint sees much of an angle. It's a very cool design. Incidentally, the factory installs a CV (three u-joints) driveshaft in the front of all of our TJs.