Uploading an InDesign Document to "Issuu Online"

I work for a small newspaper that produces a monthly catalog of homes for sale in my area. Beyond printing this free publication on a press we also upload it to the Issuu Online website so readers will have access to the homes online as well.
I took over this project for a designer that just "up and left" without leaving any explanation on how to do this correctly. The problem that Issuu Online has appears to be caused by their limitations to how large of a document can be uploaded. I am hoping that I can get my publication online by postscripting the document, but am unsure as to what the optimal presets should be. Any help in this area would be great.

At the paper we "print" to file/PostScript to cover all of our bases when creating an ad. We have set up several options to do several different things like convert an full color ad to black and white, or ensure that an ad is completely CMYK even though some images built into the ad are RGB. Once we have created the PostScript, we distill in Adobe Distiller using similar setting that further refine the file, like adjusting a black and white ad to 200dpi instead of 300dpi to ensure that the black won't bleed too much on the newsprint and create a "muddy" image.
I was hoping to setup a preset from scratch so that I knew how to fix it instead of just scratching my head wondering what went wrong after an hour of PDF-ing and uploading to the Issuu site.
I hadn't tried the smallest file size preset yet. I guess it just seemed to easy to be the fix. I tried to upload the file again today and had "heard" that one problem might be found in how the document as a whole was set up. The magazine is built in separate sections in InDesign, then PDF-ed and then placed into a new InDesign document that is the whole book. I had "heard" that there may be an issue in the way the sections are created, some of which were built by non-designers (people that think they know how to design using MS Publisher or whatever).
Still trying ideas and looking for solutions, but will get back when I can. Thanks!

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tis true
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