Hi I've been the "epublisher" for my father's publishing company for about half a year now and I (think) I've gotten pretty decent at it, and I'm also currently playing in a PTA (Pokemon Tabletop Adventures) rpg with a couple of my friends, but the Players is a big honkin' pdf with no toc so I thought hey maybe I could convert it to a epub and put in some easy browsing features and put it back up on PTA website for them to give out as they please.

However the players handbook has alot of graphs, images and special formating, That in my experience often gets lost in the conversion and can be a headache and a half to get back in place, and I haven't found a program or process that converts a pdf to an epub clean enough for what I'd want to start with( especially for something I'm just doing as a nice gesture). So I'd thought I ask you guys if you have any advice. I'm currently experienced with Idesign, jutoh, and calibre but I am willing to try any program.

Get Adobe Acrobat. You can then add a ToC to the PDF. But before you give it out, do you have the rights to give it out?

Well it's more then just a TOC that I want to add, and I want to make it easier to read on mobile platforms. I'd be giving it to the authors so that they can distribute it as they see fit so yes. It's all open source and open to the public for free.

I wish I had a dollar for every time someone asks this exact same question. Everyone will tell you many ways of getting the text and images out of the PDF. That's when you find out the limitations of ePub formatting. Adding a TOC to the PDF will save you much time and possibly grey hair.
An example. I have just turned a printed book from an InDesign file into an ePub in a couple of hours. Another day to inspect it and iron out the glitches. Last year I spent four weeks turning a printed book from a PDF into an ePub.

I would try to contact the authors and tell them what you want to do and ask if you could have the original source files for the handbook. If not I would run the PDF through ABBY Finereader to get the text and images, clean up the text in Word, save the text as filtered HTML, clean out all the garbage tags Word adds, then code the ePub in Sigil.

Of course a lot of the complex formating you can do in PDF just can't be done in ePub, but you should be able to get a usable book out of it.