Multi-document PDF reading on the iPad

I just delt with a troublesome issue and wanted to both share my experience and ask a question.
First off, I was transfering a number of PDFs from a PC to a connected iPad through iTunes. (easy)
There are a number of PDF readers out there, (Goodreader, Readdle Doc for ipad, & PDF Pro) and they all read PDFs and offer many other great features.
My issue was that anytime I try to open a PDF created from multiple documenst, it would not open and tells me that I need a PDF reader from Adobe.
- This solution is unavailable on the ipad for the foreseeable future.
My work-around was to save out each file individually from Acrobat on the PC and transfer the collection to the iPad.
It was a quick(ish) and ugly fix to get me past that single problem, but I would really like to avoid this in the future. Does anyone have any advice on fixes for this?
I would be love to hear about any tricks out there, be it iPad PDF viewers I have not tried, or Win 7 based PDF utilities that will flatten the PDF so that it can be read as a single file. I will even try stuff out and work out a solution , because the saving file individually thing is way too slow for me.
The ultimate PC based solution would be a applet I could drag the PDF file onto that would do a conversion and pop up a "Save As" window.
Please let me know if I should be posting elsewhere.
Any comments / suggestions welcome & Thank you for your time.
P

The iOS 4 update, probably in the fall for the iPad, will let iBooks read PDFs. There are lots of apps now that do PDFs, either just that or as part of other functionality. I personally like GoodReader, but there are many choices. If you get one that does "file sharing" (GoodReader does) you can transfer them via iTunes by going to the Apps tab, scrolling down to the File Sharing area, and tapping on the app that you want to read PDFs in. Then you can drag and drop or use other means to transfer PDFs, delete them from the iPad, etc.
Mail and some of the other apps also can process PDFs, but for (longish) books they're probably not ideal.

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