I'd say do both at once. An HD tranny with L67. You can find a series I cheaper then $5k for sure. You'll need to add some wires at the firewall for the boost stuff, and a boost gauge inside will be good. Otherwise they'll pretty much fit right up.
Otherwise a Series II L67 with 4t-65 HD would be the best. You could find one at around the same price as the series I, and you'd have a highly modifieable car. Use a GTP PCM and you have lots of options for PCM upgrades, and an overall more performance oriented computer.
ww.l67swap.com is a great place to start up. They have all the things you'll need, and are in cohoots with all the vendors that will be able to show you exactly what you need for this.
'06 Vee Dub GTI 2 door Tornado Red
- 2.0 Turbocharged, Intercooled, Direct Injected, 6 Speed DSG, Underbody Aero, 17" Classix
- Moonroof, Bi-Xenon headlamps, Interlagos Plaid Sport Seats, 6 Disc In-dash, iPod integration, GTI Monster Mats (winter)
'93 Bonneville SE Purple Pearl H4U package - picked up June 23, 2003, Traded-in June 28, 2007...