I’ve got 2 El Caminos, one with factory AC and the other with a Hot Rod Air unit (the company is no longer in business).
As mentioned, the factory setup works well, parts are readily available and not in high demand so pretty cheap. Only disadvantages seem to be it is big, complicated, a pain to R&R and the evaporator case on the engine side of the firewall makes it look cluttered and depending on the engine may need to be clearance for valve cover clearance. If you do go with a used unit spend the $50 for a new heater core, it is a real PIA to change a leaking core 6 months down the road.
The HRA unit in the other El Camino works as well as the stock unit, but there is a lot of fitting work to initially get it in. Additionally you will need to buy the firewall panel, a drip panel and likely have to trim down the inside of the glove box. Cost was about $400 for the under the dash unit but the hoses compressor, receiver dryer, condenser, brackets etc are the same cost for either unit.
For the engine swap I did I would go the aftermarket route again, for a pretty much stock car I would just put the factory components in. Just my 2 cents.
The work to put it in is pretty much covered in this thread.
viewtopic.php?f=41&t=25429