I have now moved dnsmasq.conf to a different location.
I figured out the FTL issue (i think). I had to compile FTL from source, based off this thread: Pihole installer: /usr/bin/pihole-FTL No such file or directory - #20 by Mcat12
However, here are the results of the commands:
pi@raspberry:~ $ ls -lh /usr/bin/pihole-FTL
-rwxr-xr-x 1 root root 1.3M Jan 7 11:40 /usr/bin/pihole-FTL
pi@raspberry:~ $ file /usr/bin/pihole-FTL
/usr/bin/pihole-FTL: ELF 32-bit LSB shared object, Intel 80386, version 1 (SYSV), dynamically linked, interpreter /lib/ld-linux.so.2, for GNU/Linux 2.6.32, BuildID[sha1]=c75e2cd421947c1ded30b0b5e7668c255cafa923, not stripped
pi@raspberry:~ $ uname -a
Linux raspberry 4.9.0-4-amd64 #1 SMP Debian 4.9.65-3+deb9u1 (2017-12-23) x86_64 GNU/Linux