First, welcome to the forum. Now where are the pics of the '66?
I am in a similar situation right now. As circumstance would have it I currently have a 3.0 and a 3.2. And I am going to go with the 3.2.
I am choosing the 3.2 because as they say, "there is no replacement for displacement." I also like the motronic engine managment system over the CIS of the earlier 3.0L engines, but some would argue that point vigirously. I think that the 3.0L engines have better low end torque than the 3.2's do, but I could be wrong on that and some changes to the chip and exhaust in the car could aleviate that issue some.
When buying a 3.2 check and see if there has been a top end rebuild where the valve guides were replaced. There has been an issue with pre-mature valve guide wear on the 3.2L engines. If you decide to go with either the 3.0 or 3.2 you have to check and make sure that the headstuds have not been broken as this is an issue with both engines. I think really you should hunt for the best engine you can afford if you find a solid 3.0L with upgraded chain-tensioners (to hydraulic carrera type the 3.2's all have this), and good compression and leakdown numbers then you should go for that. On the other hand if you find a solid 3.2L engine then that would be better. There is not a significant price difference between the two that I have noticed. Also add into your costs of engine transplants that you will probably need to look into better oil cooling for either the 3.0 or the 3.2.
I don't know what you are exactly looking for or what you budget is, but a lot of times some really good deals come up on engines on the parts for sale forum. YNUTKLER was selling an engine he would personally rebuild with some warranty, I think, for somewhere around 9K or so. That is a decent deal considering a 3.0 or 3.2 is going to cost you at least 5K and you wont know exactly what the overall shape of the engine is. You could get lucky and find a great engine that will last you a long time, or you could be unlucky and buy an expensive paperweight. There is a risk in buying a used engine even when it is from an honest seller. I am going to sell my 3.0 in the near future but I don't know exactly when something could go wrong with it. It could be 100,000 miles from now or it could be 100 I really don't know and I like to think of myself as an honest person.
Here is a really good website dedicated to transplanting a 3.2 into an eariler car a '77 I believe. Good luck with you endeavor it is a lot of fun. And I say it a lot of times but Wayne Dempseys book on engine rebuilding is full of tons of information that could come in handy.
3.2 install page:
http://www.pelicanparts.com/MotorCity/marcesq1/
Engine rebuild book:
http://www.101projects.com/911-Rebuild/index.htm
Rich