The vacuum advance should always be connected to PORTED vacuum, it's usually under the carb or on the side depending on the carb, just make sure at idle there is no vacuum present and your good to go.
The kick depends on the transmission, most have them but some older adn newer ones dont, a vacuum modulator is always hooked to MANIFOLD vacuum.
Use the exhaust cross over blocks when your sole intent is performance and not driviablity. It keeps the intake cooler and that makes more power.
The tranny fluid in the oil is a great idea, it's loaded with detergent and it will have the inside of your engine looking like it was new if you do it on a regular basis. You mentioned that you might have lost some intake material down in the pan and if thats the case just do like you said, after draining out the old oil pour a coulpe quarts of motor flush or diseal fuel till it comes out clean, then pour five quarts of some cheap oil and spin on a new filter run it about a 100 or so miles drop that stuff and pour in the good stuff and never look back.
Goodluck, Charles