Sad update here, the 'clunking' has returned with a vengance. Really not sure if it is related to the control arms or not (it shouldn't be since they're new). My sway bar is in good shape as far as I can tell, I know those are prone to cracking. Haven't checked engine mounts yet, seems more related to steering/suspension but I will check. Would getting an alignment possibly fix some issues?
EDIT: For the benefit of those who have asked, I purchased the MOOG CK80538 and MOOG CK80539 "Premium" Problem Solver Complete Arms w/ Ball Joint. Also, I noticed rickisrad recommended the police package moog "RK" series. While these are comparable in price to the moog "CK" Problem Solver series that I purchased, I have read to avoid the cheaper economy moog "RK" series (which sell for around $50 a piece) as they are inferior quality.