Yes, I've done the same thing. I top mounted the joystick so that the shaft sticks out higher. If it's mounted bellow, it's too short. I also have used US/Happ/Lorenzo style convex buttons. (my capcom FP stick, see examples pages)
I used a Sanwa in my Capcom FP stick, but then used a Seimitsu in the stick bellow cause I can get it at a much more reasonable price. This stick is also for a customer. Sanwas are nicer though, but they play at the same performance. in the Sanwa, you'll find a longer shaft, larger dust cover disk, and better switching from 4-8 way.
http://www.arcaderick.de/ sells the sticks for way to high. $35-45 USD???
You might as well get them from Ultimarc, but the shipping will be a killer. $15 for two sticks so two sticks will be about $45 to ship to the US. If you can go for the Red ball top Sanwa, then go for Ultimarc!!!
I can sell two Seimitsu japanese joysticks seen used in this CP for $14 each and I'm in the US. They are much like the Sanwa's but they don't have the disk to swap quickly to a 4 way. The plate must be unscrewed to switch to a 4 way. I also think that I can get them in red/green/blue... they come from the Capcom arcade div...
In this pic I've routed the wood out to have the plate rest right under the plexiglass