Steve,
If your redoing it, then having something that compliments the existing sensor tech would be neat to see.
Off the top of my head;
Thermal Masking (reduction of heat emissions, modulation of engine emissions to reduce signature)
Thermal Baffles (reduction of heat emissions via advanced cooling, heavy and inefficient)
Stealth Engines (built to reduce/mask engine emissions, at the cost of thrust and acceleration)
Advanced Hull Composites (EM absorbent/reductive composites, expensive!)
Stealth Construction techniques (building hulls to reduce/minimize EM cross section, expensive, expensive to repair/refit)
EM Masking (reduction of EM emissions via electronic measures)
EM Jamming (good old brute force sensor jamming, energy intensive {burns fuel}, short range, and a hell of an EM emitter at long range)
I will try and post more when I can.