I would see if the builder would you can do some work that would take extra time your self:
IE:
heads clean ports up, match to your intake runners and exhaust.

Get the cam from Webcam
Ratio rockers.

Unless you want to save them for your custom engine.

When you go for a HP increase,

If you want to change the stock demisions:

1st I would increase the compression through a small (1st oversize rod bearing) offset grind OR European pistons or gasket set(thinner head gasket)

2nd increase bore 1.5mm (watch the deck height to prevent pistons from hitting valves.  Piston cc's must be the same or a little less (increase compression)Make sure that the :pin height, ring height, proper VW offset is built into pistons.

3rd stroke increase. Here I would look into the complete 2.5L upgrade kit (@$5K, includes: head, crank, pistons, cam and rods.

 Using a matched kit prevents problems from trying to make the "stock" parts work beyond their design.

If the bore is increased correct deck height, pin height, ring height, pin offset must be maintained or problems will develope.  Increasing the stroke- offset grinding crank- bearing journels will be outside of surfacing hardening, stress cracks, oil holes mismatched, then changes to the piston are needed)
I know that FAT Performance was installing a kit (Last Dec. 98)for a customer to use with his stock FI.

Let me know if you have questions,
Robert