I have an 87 with a factory system that I recentlty rebuilt. I looked into the conversion pretty seriously when I was reassembling parts and found that it's not conducive to R134a conversion. The condenser performance is marginal at best and you have to install a paralell flow condensor for it too work acceptablly. R-12 is still available and expensive, but prices have come down a little in the past year or so.
That being said, it's posiible to swap all the components in, but it would be a major PITA to do. I had to replace the evaporator in mine and swore I would never do it again. I'm glad it only has to be done every 17 years or so! Of all the projects I've undertaken, and I've had about every part out of my Jeep since it was new, removing the blower assembly housing and getting it back in and watertight was probably the most frustrating thing I've tried. It was much worse than any part of the 4WD conversion, but that's probably because none of that involved laying upside down with my head buried under the dashboard.
I would not be surprised for you to find that many of your donar parts have reached the end of their usable life, remember they are coming off a 17 year old vehicle. The threads on the hoses are probably seized to the other components and will be difficult to remove. I had to change the evaporator, not because it went bad, but because I could not get the expansion block to break loose from it and ended up rounding off the fittings even with a Snap On tubing wrench, which I bought specifically so I wouldn't have to remove the evaporator.
If you still want to give it a try I can probably help you out because I've recently been through the whole system, but I ended up spending close to $1000, and lots of time and aggrivation, to get my 87 system working again. Just post with any other questions you might have.