Craigztoyz has answered most of your questions, but here's a couple of points:
Robstar wrote:3. Mettler (If he reads the thread haha!), were you speaking quite literally when you said the only difference between the VH41DE and the VH45DE are the 400cc? Do the internals from the latter, just simply fit the VH41DE and that's an instant 400cc?
Yes, you can literally slap the VH45DE crank and pistons into the VH41DE (rods are the same in both engines). This is what I've done with my build, pics of my bottom end rebuild available in a thread around here somewhere. However the motors are only identical internally, but have significant differences externally. These differences do not affect swapping the internals.
Robstar wrote:4. I see alot of intake manifolds being custom made, if I was to chase more power N/A or Turbo, does this mean I need to fabricate my own? Does the stock intake just not hold up?
The stock intake is pretty good for boosting torque mainly in the midrange RPMs. Tuned runner length & plenum volume lend themselves to helmholtz resonance effect.... Q45tech can tell you more. It's not really restrictive as such, and I'm pretty sure no one's done any actual testing that proves the manifold needs replacing. As far as I'm concerned, it's a mighty fine looking manifold and I'll be keeping it.
Oh also, the stock ECU is pretty good. You can desolder the eeprom and socket the board, romulate your ECU, write new maps, and burn chips for it. You only want to go aftermarket if you want to change to a MAP sensor and start adding crazy extra features to your motor... but if you just want to tune the fuel, spark, and VTC somewhat, the factory ECU will serve your needs fine.