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Ideal PDF reader for large / multiple documents. Advise please.

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iPF Noob
Hi, I bought the ipad a little while ago with the intention of using it almost solely as a PDF reader. I have thousands of pdf papers, text books etc, and I'm looking for a decent program to organize them all.

I've read a lot of online reviews but they don't seem specific to my needs. I downloaded "PDF reader" which was not the best program (and it was 4 bux...).

Here is what I need in a pdf reader, hopefully someone knows the ideal program, or can make one!

1. Program must handle thousand page pdfs
2. many PDFs have links to chapters etc within them, I need the program to maintain these and keep them functional.
3. Easy transfer from computer to ipad. With "PDF reader", you cannot import folders of PDFs, so I currently have a mess of thousands of pdfs all mixed, while I would ideally like to be able to copy the folders to maintain the organization.
4. Ability to download and organize pdf's directly from the web. I commonly want to save some articles I'm reading, but "PDF reader" (despite claiming it can do this), cannot do it from the site I use. (I am trying to save mainly scientific papers which require access via my university website).
5. Good bookmarking options to keep track of where you are in multiple documents.
5. Cherry on top, but the ability to make notes or highlight/circle things within the pdf for future reference.

Next, a lot of my text books are in the dreaded .CHM format. I tried to convert some of them to pdf but the final copies are terrible- poor formatting, no chapter links, essentially unreadable, especially since they are about 8000pages of unformatted text/pics.

Any help is greatly appreciated. Thanks.
 
Goodreader. That fills just about every requirement you have.

No idea if anything will do compressed html (CHM). I believe that is a Windows format.

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Sent on my EVO 4G with Tapatalk
 
Only PDF reader is the one and only Goodreader. It is the only one that can read 300mb+ image heavy PDF files. iAnnotate sucks compared to Goodreader. iAnnotate literally like hours to make the files to its format in the beginning.
 
I installed GoodReader a few days ago. It is much much better than PDFReader (which is 4x more expensive), but the one downside: It is noticeably slower. Not bothersome, however. And worth it for everything else.

I was able to zip all my pdfs nicely organized, transfer the zip file to the ipad and then unzip within GR, keeping everything organized.

Downsides, and things I still need in a PDF reader:

GR doesn't allow you to scroll continuously through PDFs like PDFreader (which is convenient). I find the page turning function annoying.

It is noticeably slower, for loading, searching, zooming, and page turning. Not a biggie.

I wasn't able to download my pdfs directly from the internet, I am still working on this one though. Ideally I'd like to be able to select "add to Goodreader" within Safari when the PDF opens.
I think the problem is that the PDF doesn't open as a .pdf, but rather the pdf is embedded within a page with lots of other options.

PROS:

Able to annotate, make notes (although many files won't allow this).

Bookmarking seems to work nicely.

Very powerful program, I'm still learning all its intricacies.

Lastly, I am looking for a good CHM to PDF converter. I've tried a couple of the popular ones, the best by far is the one from Softany.
However, when I open the PDF in goodreader, it says that there was a problem and I should email the file (200mb) to goodreader support for analysis. None of the text links to chapters are active, which is what I'd like in a 8000pg document.
 
Goodreader has its own proprietary PDF engine that can read very large files better than any program out there. Have you tried anything 100mb+ with other reader? They crawl like insects.

Whenever you encounter something in your browser, put "g" in front of the address you have. ex)ghttp://www.ipadforums.net

Then it will open up Goodreader and download that page.
 

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