granite00,
Interesting. The way the ocean looked didn't bother me (probably because EVERYTHING looks better than the periscope view in Dangerous Waters
) and I wanted to stay as close as I could to TorpX's original intent so I left the weather the way he set it.
Your installation order looks right. If you liked the way the TMO sea looked (and acted) then just follow fitzcarraldo's advice and delete scene.dat. To clarify: Disable ISP in JSGME first, then go into MODS\Improved Ship Physics 2.6_TMO_RSRDC_OTC\Data and delete scene.dat, then reenable with JSGME.
Have fun!