Do a

search on the word "Stroker." I wrote a summary of the quench issues a week or so back.
You can also join and search the Strokers group for the answers on
www.groups.yahoo.com (go to the main yahoogroups site and search for "strokers"). This is the web group that was formed by AMC six enthusiasts to eliminate the secrets behind the stroker package.
If you are trolling the typical web sites for information (

, PBB, JU, Rockcrawler, off-road, etc.) the probability is high that the info for the articles and forum post experience came from a discussion on this web group (other than the HESCO and Clifford performance packages). Accurate Power was a participant in Strokers group discussions as well, and offer their forged piston kits to meet a group request for a long rod piston solution. Dino on JU's Speed Freaks forum is another regular participant who brings many questions and has assembled the most accurate summary of what has proven to work. You may find that if an AMC six performance question comes up on another forum, the question will eventually get posted to the Strokers group for advice (the participants range from AMC six drag racers to Jeep enthusiasts). Rather than ask the "expert" on any one general Jeep/AMC forum, you may find it better to ask the question on the forum where most of these "experts" come for advice (the Strokers group).
The other alternative is to sit down with your machine shop and talk to the engine builder about building an AMC six. Talk about quench and compression ratio with dished pistons (ask if they have built modern era 90's AMC six engines before). The principles are no different from building any quality performance engine, except there is limited off-the-shelf part combinations that work. The machine shop will need to be familiar with decking the block for quench and machining the piston dish to lower the compression ratio (or pay for custom pistons). If you get a bad feeling about the shop's capabilities find another machine shop (any shop who builds true performance engines, more than an assembly of catalog parts, will figure out what you are talking about).
Yes, to match quench height and compression ratio you need to machine stock replacement pistons (customize the pistons) or use custom piston forgings (or you can bolt in the stock replacement pistons and make the package non-quench compliant). If you are looking for a another way around the custom piston route, you will need to find someone else to offer encouragement (and if it works well, post the package because the results have been mixed).
It's your money and other than buying a package from one of the mentioned suppiers you will have to learn the tricks to know what you are building.