[Nook Touch General] bnook:
Found some solutions.

1.) Page Turner

This is what I settled on. The sync does in fact work, what I had to do was delete every book off my device first. Then on Calibre, change the settings so it would automatically manage the metadata (on each connect) on my devices. After doing this I re-uploaded the books to my phone and Nook Simple Touch, allowing Calibre to manage these devices. Since doing this, the sync feature has worked well.

Pros:

-best, most crisp display of any of the readers I have found which are capable of syncing

-sync feature works smoothly (after loading as above)

-developer of this software is very active and responsive

-the objective developer states for designing this software is consistent with my purpose - open platform for reading DRM free ebooks smoothly on multiple devices

Cons:

-does not support custom bookmarks or notes (I am told this is planned for the next version, but timeline is not certain)

-control of interface leaves room for improvement (have to navigate through cumbersome menu to adjust font size, can't put in all the cool finger swipe controls that Moon Reader has), however, as my GF put it, the purpose is to read not to have fancy controls, and bottom line is once I get the settings adjusted the way I want, this offers the most crisp, best visual reading experience.

2.) Moon+ Reader Pro (old version, can get the old APK that Nook will accept)

I was able to get this sync feature to work after clearing device content and re-uploading with Calibre managing devices and meta-data, as described above. Not sure what problem the people in the thread I linked to in my original post were having, but I did not have this problem when using the same version on both my phone and nook.

Pros:

-syncs

-amazing control options (adjust font by sliding up and down side, assign swipes across page to various functions - I liked left to right and vice versa for skipping ahead or back by chapters, swipe up to close app, swipe down to return to bookshelf), very feature rich

-allows for notes and bookmarks

Cons:

-display is horrible on Nook! absolutely terrible. This was the deal breaker for me, as even though I loved the ability to customize and control the interface, the fuzziness, lack of contrast and crisp screen was unacceptable for prolonged reading.

-the developer is not currently interested in supporting the Nook, so there will be no updates which will change anything. All the development is going into versions that will not run on the Android 2.1 (which nook uses)

3.) Aldiko using Aldiko sync

I must confess I did not try this very hard. I downloaded the latest version of Aldiko which the Nook would support, and found the control of the interface as well as quality of visual display to be inferior to the other two options.

However, you can make this work I believe. You need the separate app aldiko sync. Unfortunately, in the more recent versions (which are not supported on Nook), you need to have root access to the device (something I was not interested in doing on my phone). I did get it to work by loading the old APK, which did not require root access for aldiko sync, and this did work. But as above, I found this option inferior to both of the others.

Hope that helps anyone else with the same questions I had. I would like it if Page Turner would become more feature rich, the very most important feature needed being support for note taking, and custom book marks.