1: Using Maelstrom 64 bit, I can spend the night in the tavern in our copy of COAS, GOF 1.2, GOF 2.0, GOF 2.5 and ERAS 2 and I see no flickering textures on the floor. I can guess that the problem might be the sea is still enabled in your location; disable the sea for that location load in your scripts, or if you do want the sea enabled, change your sea height in the scripts to make sure it is lower than the floor.
2. The original scripts tried to set ambient light for locations with a function: ExecuteTechnique("amb_tavern") But that function had no effect, and never worked from the scripts because the Storm engine did not perform that feature properly. I changed it use a message instead, during model load: MSG_LOCATION_SET_AMBIENT_LIGHT. If your location color is disturbing, either change the .col files for that location/hour, or you can set the ambient color with that message in your location loader script and the color you send will imbue that tint into all the textures of that location as ambient light.
3: The original City of Abandoned ships had lots of fog at sea. ERAS 2 has little or no fog. This is all set in the weather scripts, so if you have too much fog, change your weather scripts.
4: I changed none of the wave calculations from what I was given. The only things I changed for the sea is to more properly handle the multi-threading event responses, increase the number of supported polygons and detail allowed, and doubled the size of the wave square surrounding the ship. If your waves are too fast, too abrupt, then change your weather sea attributes for animation speed, wave frequency, sea and wave heights, sea color, etc. in your weather scripts.
5: The showWindow.aspectRatio attribute does not affect anything in the original Storm engine and does not change anything in the GUI screens; that attribute is only used in two functions: RecalculateVIcon and RecalculateVIconScaled. Those two functions only change the icon sizes displayed in the spyglass and battle interface HUD icons, nothing else. The original COAS cd also stretched everything in the character GUI interfaces, because it presumes a 4x3 display and everything was defaulted to assume 800x600. Maelstrom, by default will resize the screen elements (except a background image, which will always fully stretch) in the GUI by trying to retain the GUI element's WxH ratio, but within the actual monitor's resolution. For example if you define a 800x600 box in the screen, but your monitor is 1920x1080, the box will expand to 1440x1080, still the same ratio as it was defined in the .ini file, but fit within the current display resolution. A 400x300 box would expand to 720x540. If you want everything to stretch like the original cd for COAS does, adding noresize=1 to all the screen .ini files will cause Maelstrom to act just like original Storm and stretch to fit the entire screen. Otherwise, it will resize as I described in my 800x600 box example, turning it into a 1440x1080 sized box in a 1920x1080 screen. There was a bug in the table column width calculation, but that is fixed in the next update.
If this is too much trouble, or still unsatisfactory, then perhaps just use the Russian version of the old Storm, since that appears to be your preference anyway.