I would consider the Stage 1 Vishnu setup($2495) or the Stage 2 from TurboXS($2099) if you looking for a quality proven safe and realiable solution. If I'm not mistaken both of these stages build on to the stock turbo/intercooler setup.

You could also potentialy build your own stage kit possibly saving some money there and have Mastro Subaru in Tampa dyno tune your specific setup using the ECUTEK reflash system.

I think you're going to have a hard time upgrading the turbo and intercool with a $3000.00 budget considering:

$1000.00 Turbo upgrade
$1000.00 Intercooler
$500.00 Injectors
$150.00 Fuel Pump
$1000.00 ECU
$???.?? Uppipe/Downpipe
$???.?? Gauges
$???.?? Installation