It's been a long time but as I recall, the flags.dat in the
Improved Convoys mod is the one you will want to have so enable that mod after
Habor Traffic. I assume (and hope) you're using
JSGME to add/remove mods from SH3.
I used to play SH3 1.4b with GWX 1.03 using an nVidia Geforce FX 5200 128MB card with little trouble. The main thing is to make sure your AA and AF are set no higher than 4x, then uncheck "High Quality Textures" and set "Particle Density" to no more than 60 in the game's Video Settings.
You're still likely to have lags and stuttering with big effects, such as a ship exploding, but there's not much to do about that. Also, avoid using too many "eye-candy" mods.
The Harbor Traffic mod may cause you problems due to all the extra shipping and activity that has to be rendered by your video card.
Good luck and sink 'em all, Herr kaleun!