My experience with trying to get a shop to do R-12 may be relevant. You'd be hard pressed to find a new compressor that will permit R-12 to be installed AND still be warranted. Since 134a is the "replacement" for R-12, and the CompressorWorks compressor says "for 134a" and to use PAG oil, then the shop was basically meeting the requirements to warranty the parts used to do the repair.
The CW compressor may also have a lifetime warranty, so hold onto the receipt.
The prices look reasonable. Not rock bottom, but fair enough. The shop did state a flush of "debris" from the system and replaced the right parts, so the repair seems okay with the exception of them not fixing the fan.
That factor alone would make it very hard for them to measure the proper cycling and cooling.
The red cap is a picture of the 134a high-side port, so they can measure the system pressures. I've attached a link that compares the pressures from R-12 and 134a.
http://www.ackits.com/aacf/ptchart.cfm
The R-4 compressor was designed for R-12, so it doesn't work optimally with the higher pressures of 134a. Higher pressures = more work = more drag on the engine = higher coolant temps = less efficient cooling due to the proximity of the radiator. This doesn't even consider the lower efficiency of the 134a compared to R-12, so yeah, R-12 is better in this application (but see above for possible reasons the shop went with 134a).
Now that your fan is working, I'd recommend taking it back to the shop and getting them to check out the pressures.
A good wash of your condenser and radiator may also help.