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Edit /etc/pkgmk.conf. Change this part:
# PKGMK_SOURCE_DIR="$PWD" # PKGMK_PACKAGE_DIR="$PWD" # PKGMK_WORK_DIR="$PWD/work"
To this:
PKGMK_SOURCE_DIR="/usr/ports/distfiles"
PKGMK_PACKAGE_DIR="/usr/ports/packages"
PKGMK_WORK_DIR="/usr/ports/work/${PWD##*/}"
Finally create the directories:
# mkdir /usr/ports/{distfiles,packages,work}
Have a close look at the mismatch. If there are lots of new files, it's probably just because you have some software installed the packager didn't, which is no problem at all. In this case, just ignore or update the footprint (see the pkgmk manpage) and install it. If you're missing a lot of files, make sure you have all dependencies installed. Also make sure you built the package as root.
The md5sum is a security feature, so you shouldn't just ignore this one. The package you downloaded could be manipulated. But there are other reasons why this can happen, without a malicious action: the download might have failed (try to decompress the tarball to see whether is is corrupt), or the requested file might have been changed on the server without its name being changed; this usually happens for things like theme-packs which change constantly without getting another name.