IPad - Digital Magazines, converting PDFs to RGB.

Hello everybody,
I happen to be setting up a workflow for some printed magazines in italy, that launched digital editions of the magazines online (Classic browsers but also iPad app). Basically they need their prepress pdfs to be published on an online interactive application.
Here it is so far:
1)     Get PDFs from Prepress: 300dpi - Iso Coated FOGRA 39 - minimum 5mm bleed on each side - v1.3 Acrobat 5.0.
        Usually 200-300pages - usually pretty heavy (1-2gb). Usually around 100-150 separate and numbered PDFs.
2)     Create a single PDF file with Acrobat 9.0 from all the prepress files.
3)     Run a little script I found online (Crop Pages) that basically sets all the boxes (CropBox,MediaBox,CropBox...Etc) to a certain size.
        Basically it's a little tool that anchors a certain box size centered on each page, and crops it.
        Not very accurate, but better then manually cropping 300 pages.
4)     Run Preflight on document: Online publishing (Optimize for quality). Analyze and Fix. This drastically reduces file size.
        PDF Version is upgraded to 1.6 Acro 7.0
5)     Run Document Processing: Create links from URLs. This basically creates acrobat link areas wherever it finds a www.xxxxxx.com format.
        (absolutely mandatory, they want their digital magizine to be fully interactive)
6)     Briefly check for errors, missing links, etc. Run preflight for page size and CMYK objects (they make the iPad go nuts).
7)    Manually add videos and galleries and the rest of the interactive objects. Afterwards, send the PDF to web agency.
Despite the whole ordeal, there's still lots of things that aren't working!
On point 1 all the pdfs I receive present the infamous 1px white hairlines in between trasparencies of the 1.3 pdf version.
Most of them disappear  upgrading to Acrobat 7.0 but some of them make it all the way to the iPad edition!
Is there any known way to get rid of this 1px white hairlines once and for all?
On point 3 the tool I use to crop the PDF pages is pretty rudimentary and not very trustworthy.
It forces me to double check every single page to be cropped the right way.
Is there any known tool that can set (in batch) all the boxes, especially Media and CropBox to the size of the TrimBox?
Can it be developed? The Idea is 1. Get Trimbox - 2. CropBox=TrimBox- 3. MediaBox=TrimBox on each page.
On point 4 the preflight profile does an awesome job all by itself and during the process it converts all the CMYK in RGB.
Despite this, the colors seem to look dull. I understand this is because, being printed magazines the CMYK colors are for printing purpose
and can't be as bright. Converting (relative colorimetric) I get kind of washed out colors.
Is there a conversion method that can boost the saturation/clarity of my RGBs in the PDF?
This is to get their online application to be a little more "attractive". It's a shame to not take advantage of a bigger colorspace (RGB).
On point 5 last but not least acrobat creates rectangular link areas that in most cases do their job but completely mess up on
curved or oblique text. Basically if the link follows a circular path or lays on an angle acrobat creates this massive rectangles around it.
Is that it? Just plain rectangles?
Is there a way, in acrobat or even in indesign, to create circular or polygonal shapes for the link areas?
Sorry for the epic length of this post.
Hoping that this could be helpful to others (There seems to be no info about this stuff on the internetz),
I thank you all in advance.
I can provide screenshots if needed.
A

Hello, A
As you have been said, if you start with that kind of flattened PDFs, it's rather difficult to reach an apple-pie PDF for what you want: everything is chopped-up. If you could set a workflow where the original creators of the PDFs would generate a second batch of PDFs for the web, that would be the best and, in the end, the easier system.
In any case, the odd washed-up colours are usually due to a bad setting of the colour management at the time of making or repurposing the PDF. With a proper set up, aiming at sRGB should render a PDF that looks on screen rather similar to the printed final version (taking into account a reasonable screen, not a madly wacky one, of course).
You do not specify what is the software used to arrange content and to make the PDFs, but I guess that, if the magazines are 'big enough' (that is: they are not a some kind on enhanced newsletter), you could even set some kind of automated workflow (take a peek to tools like Switch —Enfocus— of PDFColorconvert —Callas—) that would be extremely easy to use.
As for the interactive side of your questions, you'd be better served if you make this kind of questions in a forum like the Acrobat, Dreamweaver or Flash ones.
Hope it helps
Ciao

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