[Will]

The vacuum advance can be run from either manifold or ported vacuum, but it will depend on the engine. Low compression engines or engines with big cams tend to like LOT of initial advance and one way to get that is to run the vacuum advance to manifold vacuum. If you hook up a vacuum gauge and go drive around, first to a manifold vacuum source and then to a ported vacuum source you'll see that you have vacuum in your manifold at part-throttle cruise which is where your engine needs the vacuum advance. It may be more or less than the ported vacuum source depending on a number of factors.

In short, experiment with your timing to figure out what your engine likes best. Both of my cars like ported vacuum with high initial advance dialed in and a short mechanical curve, but high compression engines might have a hard time cranking over with a lot of initial advance dialed in so hooking them up to manifold vacuum is a good way to effect a "timing retard" until the engine is running. I know several engines that run real good like that.

As for the trans, definitely hook it up to manifold vacuum. That dropping out of gear you experience when it's hooked to ported vacuum is extremely hard on the tranny and chews your clutches up with all that engaging and disengaging.