Regarding the token signing cert, if you use WinCA on the 2008 version, you have to be certain that you don't get a certificate that uses the new ECC (elliptic curve) key algorithm and uses a "normal" RSA pair instead. .NET still does not understand ECC keys and thus the .NET code in ADFS that does the signing doesn't see the cert as being valid with the same error you reported.
Laura Hunter ran into this issue. I had never heard of it before. :) Not sure if that affected you or not in this case.
Glad you found some answers to the other problems as well. I remember when Michelle was working through the lab and found all those problems, especially the issue with the IIS 7. I didn't have much experience with it at the time and we had to ask one of her friends instead. Luckily, she has many very smart friends and was also kind enough to document all the issues.
Thanks for detailing out the problems and solutions. Hopefully it will help others as well.