Vaccuum lines in boosted applications?

Sounds like an interesting project. For my supercharged 306, I'm using the stock 5.0l PCV system with a power-brake booster check valve in-line on the vacuum side. There are lots of other strategies, including oil separators and fancier check valves, but the power brake booster check valve works well for modest boost levels (I run up to 9-psi). You'll probably want to run a PCV system and not eliminate it - otherwise you'll likely push some oil out somewhere, even if you've got a valve cover vent (the dipstick tube is a common spot for oil to mysteriously appear). Check corral.net's supercharger forum and you'll find lots of advice on this.

Not sure about the timing advance or trans modulator - that's outside of my experience.