Well I'm flattered but there are any number of people here that give great advice, Lancetkenyon above already having proven himself as being a great source of tech info.
On the shocks being dented, that is due to the axle being rotated for a CV driveshaft which moves the shocks in closer to the axle tube. You can do one of several things to fix that... 1) flip the shocks upside down so the strut is at the bottom. That will give the added clearance you need. Most shocks work fine mounted in either direction, only a few don't. The many shocks I ran can-up on my last TJ all worked fine mountd in that direction. Or 2), as Lance suggests, you can simply grind additional clearance on the lower spring bucket. However, I would not install any type of aftermarket shock extender bracket which just provides enough added leverage against the mount weld to tear the lower shock mount away from the axle tube.
Regarding the control arm lengths, they are identical between the TJ versions of the D44 and D35c. The axles even use the exact same tube diameters (thickness too) so there are zero dimensional changes for the brackets on the D35c vs. D44. Examine the axle end of the control arm brackets, they are known to bend or tear away from where they are welded to the axle tube. Either of those can cause the control arm length to look wrong.