[Faterson]

Originally Posted by crashnburn

ALSO is there any way for me to save/ backup and restore my Highlights already present in my iBooks.

Don't know because as soon as I saw iBooks for the first time, it was obvious to me this wasn't a serious app for reading either EPUBs or PDFs, so I threw it away. The best for you, I'd say, would be to cut your losses asap and ditch iBooks for good.

Originally Posted by crashnburn

Is there a certain iPad Stylus you use/ recommend (please not expensive) for Highlights/ Annotates? Or just your fingers?

Nope, no stylus here. Steve Jobs was correct in saying that people have 10 styluses on their own hands, so why should we need an artificial one? Making highlights and annotations with fingers works perfectly both in Marvin for EPUBs, and in GoodReader for PDFs.

Originally Posted by crashnburn

Would that allow me to Sync with my Windows 7 laptop?

Of course...

Originally Posted by crashnburn

- iPad
- Read, Highlight, Annotate > Be able to copy/ move these annotations to the Laptop, somehow.

Yes, very easy to do from both Marvin and GoodReader.

Originally Posted by crashnburn

- Preferably they are visible AS IS from iPad to Windows / Desktop Program.

Yes, definitely, GoodReader allows you to do that with a single tap of your finger.

Originally Posted by crashnburn

Key question? - Does Good Reader..
- Store Annotations/ Highlights as an Independent Layer/ File or
- MERGES them into the Original File
(Or allows both).

Yes, GoodReader gives you both of those options, and adds a third (email summary of annotations).

Originally Posted by crashnburn

I will have to check this out.

Definitely! You can't miss with GoodReader -- it's the premier PDF app on iOS, so you can just go ahead and buy it. I think its AppStore reviews speak for themselves.

GoodReader has what some perceive as an inelegant or cluttered interface, but other than that, it's fabulous. Please note that the entire interface of GoodReader completely disappears as soon as you open a PDF file -- which is, in fact, one of its nicest features. You really feel as if you were holding the original book or sheet of paper in your hands -- GoodReader gets out of the way and lets you focus on the PDF file only.