Has anyone replaced the standard lower control arms on a 66 SS or other chevelle with the boxed ones, added the sway bar and put in the heavier spring thus increasing the rear ride height about 1 1/4". Was wondering what this did to the angles at the u-joint, if any increase in vibribration of drive shaft was noticed, if it was necessary to shim the support for the transmission and or the upper control arms to get the angles withing specifications?

the 1 1/4" taller springs sound like cargo coils,and no you do not need to shim ANYTHING
I've done the F41 conversion on plenty of Chevelles and Cutlasses,and again,no reason to to do what you asked about.

Was there a F-41 option for 66 chevelles or did all SS come with the F-40 suppension?

No F41 in 66 , without checking I would suggest the F40 or 41 spring pbly are shorter than std springs so not sure where you get info they raise car .... they are thicker wire therefor stiffer and may raise car but ........ check out the Chassis manual for proper info then go to a Moog catalog to find the closest replacement spring ........IMHO these cars work better with stock springs ( not too stiff) and good adj. shocks and bushings for improved handling ...no need to shim anything unless you go to extremes with really tall/ stiff springs ...yes very easy to add stiffners / inserts to your existing control arms andinstall the sway bar from 66 442 etc works fine .don't go too big if you don't upgrade the front bar ......what are ou trying to accomplish ???