D13. Really?
I usually leave loop animations unchecked, and use binary instead of S&B templates. SHould give you smaller file sizes.
Textures disappearing is pretty simple.
Check the materials tab... if you have more than one material in there, then it won't be textured in FPSC. Just before you export, delete ALL your materials, then create a new one and assign that to everything. Should solve the dissapearing textures.
As a point, the info That D13 posted is already in a thread by a guy called Manofart, he left a long time ago, but I guess the thread is aptly named :
Help export milkshape model