1) no direct links to docs/PDF's worked anymore.
For example... www.mydomain.com\Portals\1\PDF\document.pdf This does not work with URL rewriter enabled on my site. It will work if I try the LinkClick approach, but I prefer not to use this.
Correct. This is due to a change in DotNetNuke 5.6.x. They tried to fix it in 5.6.1, but supposedly it will be fixed properly in 5.6.2. Nothing we can do about it.
2) I have a document.html that sits in the Portal\0\ folder. It renders fine with no AF URL rewriter, as soon as I turn it on the document brings up a 404 error.
Same as above.
I am not sure if its my setup or not, but both of these don't work with the URL enabled. I would love to get the URL Rewriter working with out the above issues.
Once DotNetNuke fixes what they broke it will work fine. Basically, DotNetNuke made a change that causes a 404 to occur in the default URL Rewriter for any page request that doesn't look like a typical dnn page.
Again, none of this is a bug in the AF ReWriter.