Ok 1st of all the 2 shipyards are exactly what i was going to use. Along with jupiter station, and the subspace relay (the SoA 1 version which IMO is a better model).
I have a different model of the TMP era shipyard. Sins doesnt use transparencys on ships, and structures. Except for particles, and FX, and the model i have doesnt need any transparencys.
I am using the TMP Orbital Complex as the trade station (my own model i am building for the mod). No offence, but i dont like the model that you are using for the trader station. I would avoid non-canon if possible when there is perfectly good canon. FYI i will be using the merchantman as the trade ship.
Regula series stations for the civilian research
Jupiter station for military research
Nice effort there. I support, and endorse this 3rd party add on. Good job 
0.03 wont have any stations, but 0.04 will focus on putting structures in the mod.
Disable "use ship highlight filter" in your options\effects. that will get rid of the overly bright ships in the mod.