Wow. Thanks for the pictures. It's shocking that you'd get a new core that's not perfectly sealed.
I'm surprised that FR sent you the core directly. My experience was that they insisted on sending the new cores to a dealer and they would have to do the installation.
I hope that you got it completely seal up and that you won't have the problem again.
I asked about fitting the new style bed doors (with the permanently attached canvas) on my 2010 but the dealer told me they don't fit.
2011 Rockwood Signature Ultra Lite 8293SS, 12K Equal-i-zer
2016 Ford F-250 XLT SuperCrew, 6.2L, 4x4, 6'9" bed, 3.73
2010 Rockwood Roo 23SS (2012 - 2014)
2009 Ford F-150 XLT SuperCrew, 5.4L, 4x4, 5'6" bed (2012 - 2016)