I'm not familiar with any of the newer (non)freons other than 134a. As you stated, there are probably multiple types of 134 gas/refrigerant. My knowledge of AC is as follows (my apologies to anyone that has tons more knowledge than me) When retrofitting 134 to an original R12 system, the drier, and hoses, are not compatible, long term; nor is the oil in the compressor. You didn't say how many of your components were upgraded other than the fittings. I mentioned this because you sounded like you only wanted to deal with this once.
I had my daily retrofitted and all they did was change the fittings and the oil in the compressor. But, I didn't care about how long it was going to keep. I'll only have the car for a few years more.
I also know that 134a does not get as cold as the R12 and therefore, if you can upgrade the condensor to a larger one, you'd be doing yourself a favor. Again, it all depends in how involved you want to get. The air in my daily was pretty cold and I kept the stock condensor.
I also had the system retrofitted in another car, an 88 T-Bird. It was done by the same shop. I'm a bit disappointed in that one. Again, they only changed the fittings and the oil in the compressor. It doesn't get near as cold as it did before and I know I have a leak somewhere because I have to add another can of 134 every summer. But, this is only a summer car and I can live with it.
What I'm doing on the Cougar is starting from scratch. I'm not concerned with originality so I bought a complete aftermarket kit from Vintage Air and it is totally designed for 134a. It includes all the hoses, evaporator/heater/defrost unit for under the dash, the drier, the condensor, switch panel and all the fittings. I'm using a brand new late model Ford compressor because it fits my brackets. It also uses electronic servos to open and close the vent doors in the system so it is true "climate control." I'm plumbing it through my factory vents in the dash.
Now I'm not saying that you should go this route, that's just what I did. I know that they also offer what they call a "sure-fit" kit which is supposed to be a direct replacement for a Mustang or Falcon. It should work on a Cougar as well. I looked into this unit but it still uses all the vacuum modules to open and close the vent doors etc.
The bottom line is that they are great people to work with and would probably answer any of your questions even if you don't buy from them. Here's their web address:
www.vintageair.com
Sorry for my long response. But hopefully some of the info helps. Good Luck.
Mark