EndNote Mac X7 PDF Problems and Questions

I am running X7.3.1 on a MacBook Air with 8 GB RAM, running OS X 10.10.4 Yosemite.  My EndNote reference library contains roughly 5000 entries.

I need to use the EndNote built-in pdf reader to annotate attachments.  I have noted that on long documents (e.g. 153 page review paper that I am presently looking at) , the EndNote pdf reader either displays blank pages or partially rendered pages with either the top or bottom portion of the document “cut off” with a white bar.  While the EndNote pdf reader is rather primitive, it appears to be the only way to get EndNote to index annotations for later searches.  From a perusal of this forum, the display problem seems to have been a long-standing issue.  What is causing this problem with pdf display of moderately large documents?  Is there something that I could do to prevent this problem?  Large papers are not an exceptional situation any more and this limitation for your PDF viewer causes a huge inconvenience.

A closely related question issue regards use of the Mac OS Preview reader for documents stored in EndNote.  When I use Preview to read documents and save annotations, those annotations are not indexed by EndNote for later searches.  For example, if I attach a ‘sticky note’ annotation containing a phrase like “PROPENE IMPORTANT” to a pdf from within Preview and save that document, the ‘Search PDF Notes’ function in EndNote will not find this note.  This blindness to Preveiew annotations does not appear to be a matter of allowing the EndNote search indexing to ‘catch up’ to the changes.  Is there a way to force EndNote to index annotations to PDFs made outside of EndNote.  If you guys aren’t going to fix the built-in PDF viewer or add full-screen viewing capability for Mac OS, then you should at least not lock out annotations made through third-party pdf readers.

I am replying to my own posting, with what I think is a partial solution to my difficulties.  Unfortunately, I seem to need to spend more time researching the tools I use for my research (nanoparticle catalysis) than the actual research itself!  

I would have hoped that by now, some company would offer a comprehensive software system for reading and annotating PDF materials that could be used accross platforms (laptop/desktop/tablet).  Many claim to offer this functionality, like EndNote, Sente, or Papers, but note offer this capability without complications.  All of the aforementioned appear to be trying to gradually herd their users into a paradigm that requires access to research libraries stored on subscription-based server space through a web portal, rather than locally stored documents.  I suspect that this emphasis is the root cause for so little effort being applied to making the standalone programs better.

My own institution, Virginia Tech, site licenses EndNote for student and staff useage.  Consequently there is a strong bias here for encouraging us to use EndNote and discouraging use of competing products.  EndNote on the Macintosh platform looks old and is cumbersome to use, particularly in comparison to the next two closest competitotrs, Papers and Sente.  The iPad couterpart to EndNote is so limited in its means of synchronization to the desktop library as to be completely useless.  While the iPad was promising as a platform to read literature, it is a dead end without a better system in place to exploit its capabilities.  Consequently I have elected to stick with EndNote in spite of its shorcomings and use an ultrlite notebook (MacBook Air) to read and annotate literature from this point forward.

A casual perusal of Apple support forums reveals rather quickly that the OS X Spotlight search engine will not index pdf annotations.  Without the ability to use searches for annotations, highlighting literature is a useless exercise in painting documents.  The solution I have arrived at is to use the freeware application Skim.  I was vaguely aware of Skim over the last few years but I never took time to really study it until yesterday.  Skim stores annotations in a separate text file that Spotlight will index and search.  I set the default PDF viewer in OS X to Skim and use it exclusively for reading and annotating literature stored within EndNote.  Given the shortcomings of the EndNote built-in PDF viewer and the glacial pace of getting improvements on the EndNote program itself, this approach seems to be the best short-term solution.