OK, I've got FOTRS v1.3 loaded and ready to play. First thing I've done is check max-peck's mod Razzle-Dazzle (I coined a Japanese name called Kamafuraju Maru, but it's his choice). Some screenies from June, '44 using v1.3.
Now something that definitely needs to be improved and brought up to TMO standards. As you can see by the picture below the fire on a damaged ship looks so v1.0. I much prefer the TMO look.
FOTRS v1.3
TMO v2.5
XTBilly
I can't confirm the ticking noises you've reported just using v1.3. Unfortunately, I don't don't know how too merge the sound files from v2.0 2ith v1.3. Contact me via PM and give me a crash course. Just a random thought, could it be a difference between sound cards? I'm using a Creative SB Z card. What kind of sound card arte using on your computer?