A competent alignment shop can do the alignment with the right equipment. Setting toe in is easy (simple jig or tape measure), adjusting camber is a little tougher (angle gauge), but adjusting the caster is a PITA with out the right equipment. Having the camber or caster even a little off will cause a bad annoying pull. Therefore, go for the four wheel alignment so you know for sure that nothing is wrong with the rear components like bushings and the big ball joint that is high up in the center. The extra few dollars will give you peace of mind if nothing in the rear is found bad.
If you go for shocks, check the forum for the best Heavy Duty quality so you avoid the Junk like Monroe and their bottom of the barrel competitors. Selling a shock or strut with a 25,000 - 50,000 mile life expectancy like Monroe does should be considered a criminal act with jail time

. Some shops like to sell cheap crap to keep their business flowing, when I was in the epair business, I would not sell crap parts, did not like the warranty problems.
Congrats on getting a CRD and go on the slay the Bean Counter Engineering mission with all your Mods and upgrades, then you will have a great Jeep.