I'm pretty sure that PDF is a red herring (has little or nothing to do with crash issues). Using word2011 instead of word2016 may be a work-around to avoid crashing. Details below. 
I think the pdf problem is a seperate issue that has nothing to do with the crashes of word2016 (15.x) and/or Endnote 8.1.
Assuming the pdf issue has to do with "highlighting text is misaligned", mentioned elsewhere. This is a known-issue that has been reported to Apple, and happens with other software besides Endnote. 
Here is why I think the pdf issue is not related to the crashes or word2016 and/or endnote.. Have mac osx 10.12.6 with all updates, and it has both word2016 (with all updates) and word2011 with all updates (= version 14.7.7 (170905) = the final update for office2011, since support ended Oct 10, 2017). 
Word2016 crashing several times daily when using Endnote 8.1. But one same computer, Word2011 is working fine. If the pdf problem was causing the crashes, then why does word2011 seem to work fine on same mac where crashes happen with word2016? That's why I think the PDF issue has nothing to do with most of the crashes reported on this forum that have been going on since at least May 2017. 
Note: I don't know if word2011 will work on osx-10.13 (high sierra): probably not. But if you have 10.12 or eariler, you can try word2011. If you do not have word2011, you can still download the installer and the culumulative updater for office2011 (you probably want to install *only* word, and not excel-2011, not power-point-2011, and certainly not outlook-2011 !). 
from these 2 links at https://macadmins.software/ 

http://officecdn-microsoft-com.akamaized.net/PR/MacOffice2011/en-us/ MicrosoftOffice2011.dmg 

https://support.microsoft.com/en-us/help/3212225/description-of-the-security-update-for- office-for-mac-2011-14-7-7 

(I used to have a site-licened word2011, and when re-installing the installer found the old site license for it.) 
I'm not sure if word2011 will work on high-sierra (10.13), but still seems to work fine with newest endnote 8.1 on 10.12 (sierra) and earlier 10.11. However, there will be no more security updates for office2011, so using word2011 should be seen as temporary workaround until the crashes with word2016/endnote8 seem solved. 
I would be interested in hearing if others have found that using word2011 lessens crashing or not. If it does, then we should try to submit detailed bug reports to endote, including steps to reproduce the crash, crash reports. etc. 


http://officecdn-microsoft-com.akamaized.net/PR/MacOffice2011/en-us/MicrosoftOffice2011.dmg

https://support.microsoft.com/en-us/help/3212225/description-of-the-security-update-for-office-for-mac-2011-14-7-7