I'd say a bit more than that for parts, gearbox can be anywhere from $400-$800 depending on if its R32 or R33GTR (assuming you have an awd stagea). A good clutch is going to be at least $500, most likely more. Then you get to your interior parts, factory manual stagea bits are pretty rare and as such as are expensive, it's hard to put a price on it because over the years I have seen manual consoles go for a variety of different prices, but the cheapest I have personally seen for just the manual centre console parts, with no other interior bits, is ~$600. And there are so many little costs that you dont think of initially, things like flywheel bolts, gearbox oil, etc, it all adds up
All in all, I would budget a minimum of $3000 including labour, but would expect it to cost more than that. Thats going off my personal experience, after spending almost a year collecting parts and finally getting the conversion done a few months ago