Changing the colour on the settings options made it much easier for me to see them.
Thanks for the heads-up on where those files were stored.

"All" I did was (please don't laugh):
a) Run emelfm2 as root from xterminal

b) Browse to the folder mentioned above and copy the image files I wanted to change over to a working directory on my internal memory card (so I had the original ones should I mess something up). FINDING what image files I wanted to change required me to go through them one by one (viewing them through emelfm2.

c) Emailing the images to me (still haven't set up tablet-to-PC file transfer..sigh..)

d) Opening the images in photoshop and do a colour-replacement

e) Emailing them again

f) From modest mail saving them to a working directory

g) with emelfm2 copying them from my working directory to the flipclock directory.

Ta-da!

Attached below is a screenshot with just the AM/PM setting changed to a darker colour.