It's actually not that big.
At about 12x15 inches, it's the largest "hobbyist" PCB I've seen in a long time.
The original 6502 was 168 x 183 mils, so this is about 6000 times larger.
It looks like they did it at OSH Park too. 12x15x5 = $900 for three boards. I love OSH Park, but I would go with the cheap guys for the first go-round on this board.
I spec'd doing this myself using a similar discrete component approach. Some back of the envelope estimation put the effort at ~2 years of hobby time and about $2K in hard cost. That was the end of that :-)
Supercool to see someone followed through and made it a reality.
I had given some thought to doing this myself also. But my first thought was change the design from NMOS to CMOS. Yes, you double the number of transistors. But at least it will run faster and you won't have to bother with those arrays which I think takes away from the project, frankly, having any non-discrete components on the board. But this guy did it. I didn't. That is a very expensive board. I think the amount of cost is rather less than what you spec, through. Even at say 9,000 transistors, that is reel and a half of 2N7002 and BSS84. Those parts, roughly, are $100 a reel. So $300 for parts total, and get the boards from China on the cheap.