I am not set on the drivers drop. DO you have pan to driveshaft clearance issues as stated before? I was kind of thinking the same thing as dana 300 cost verses an atlas t-case. I like the dana 300 due to its small size and the fact that I can clock it flat. Like I said in the start possibly waggy 44's. Which I am thinking might be a good choice. Not full width but a little easier to work with.
There are tranny pan issues. I'm running a Six States CJ style driveline and it clears the pan pretty well. It's tight, but no contact anywhere. I'm running a Chev 60. Your experience may vary depending on where the pinion-yoke is with the axle you choose to run and how you mount your engine/trans (I believe I'd offset my powertrain an inch or so towards the drivers side if I was running a passenger drop or an inch or so towards the drivers side if I was running a drivers drop if I ever do another one). Worst case, you just run a pillow block/carrier bearing on the frame to work around that.
The CJ driveline is quite puny looking, but I've really never had any issues with it at all. I've broken some u-bolts on the yoke before, but that was more of a driver/maint. issue IMHO than anything else.
I like to run a stock axle with readily available shafts. I'm not a D44 fan at all, though. IMHO, they're good up to 35" tires and after that I'd rather have a bigger axle joint. I found my front axle and built the rest of the rig around that pretty much. If I were building right now, I'd take a good look at running some RAM D60s (possibly even a matched set of Super Duty axles, but they have the stupid F*rd bolt pattern rather than the traditional 8 on 6.5" that trucks have been running for 50 years). I think they are not 35 spline at the diff, though? They have the bigger axle joint and are relatively cheap. I don't mind the unit-bearing at all.