PDFs in iTunes not transferring to iPhone or iBooks and cannot be deleted

I have a few PDF files that I added to iTunes which show up in iTunes under books, but when I either click select all or select those specific books they WILL NOT sync to the actual iPhone. They also WILL NOT transfer to iBOOKS and even worse while they appear in the iTunes library as selectable for copying to devices there DOES NOT APPEAR to be any way to delete or find them.
HELP!!!
I am guessing that the problem has to do with these PDF files NOT being totally compatible with iTunes or iBooks and so they were uploadable, but once there they are stranded and unusable.
Does someone know:
1. How to find these files and delete them from iTunes
2. How to get them into a format that will actually work so I can read them on my phone and other Apple devices.
I am using an iPhone 6 plus with 8.1 and a Macbook Pro with the latest version of Yosemite. I believe that my iTunes and iBooks are also the latest versions.
Thanks.

I have an update. When I convert the original PDF files using CALIBRE to EPUB format (the mac format). I am able to get the files to import directly (ie be added to library) of iBooks and then to iTunes and my phone. I think this confirms that the problem is likely to be one of file incompatibility. However, the file is NOT totally incompatible and so will show up in the part of iTunes where you are supposed to be able to click on it to add it to your device. The problem is that since its not completely compatible clicking on it WON'T allow it to transfer to your device. Fixing this either requires converting this PDF to another PDF format that is compatible, or better yet just convert it to EPUB which presumably will be MORE compatible and allow you to do more features in iBooks (such as resize the fonts etc).
I still have the problem of figuring out how to find and delete the original PDF files which are clearly not any good. I suppose we can go to the root finder level, but where should they be as I don't see them in the iTunes books library?
Any suggestions?

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