Mechanically it's the same. Incorporating the trans and DIS wouldn't be dificult, just a lot of work. You'd have to swap over the PCM, wiring harnesses, vacuum hose harnesses, etc.
Mechanically speaking though, you could use the long block assembly (block and heads) and put your stuff on it. The Gen 1 and 2 upper and lower intakes are different from the Gen 3, but bolt patterns are the same, so you could swap your originals over. Same goes for the distributor. The Gen 3 and 4 DIS Vulcans still have the hole and cam gear for the distributor, they use it for the cam sensor/synchro shaft. Your distributor will bolt right in.
Other than that, I can't really think of anything major. Since you already have a Vulcan though, you'd be able to swap parts over as needed.