Running 5.38's in a D44 is pretty common so I wouldn't really worry about it. I've heard of people running 5.89 in them as well.
If you're wanting to go stronger then stock shafts then go Alloy. If you want to run 33 splines then you might as well go with a Ford 9 or Dana 60 as you are shifting the possability of breakage aeay from teh axle shafts to something else. Optimally though you're weakest link should be the U-joints.
I was mosly thinking the rear. I am pretty sure the my front is about as strong as I can make it without going to a D60.
I have Alloy shafts in the rear, so maybe it's fine. I guess I am paranoid about breaking a shaft. I am pretty easy on the throttle and don't let it bounce. Maybe a set of spare shafts would give me peace of mind.
I run 1310 joints, the axle end of the rear shaft if a 1330. I have spare D-shafts F&R.
I have heard that Currie Ent. does not recommend the 35 spline shafts with their HP 9 with the 8.8 gears because they have had lots of R&P failures with the larger shafts. I guess the smaller 31 spline shafts will twist a fair amount before failing and absorbs some of the shockload and helps keeps the R&P alive. While the larger shaft does not twist as much and the R&P fail before the shaft.