There is no 6 speed manual transmission Honda makes or has ever made that will fit into a Prelude. Even if you could get the Civic Si trans to fit, Prelude engines rotate the opposite direction from Si engines (look under the hoods of both cars, you'll see the accessory motors on opposite sides).

The only possible way is to have someone build one from scratch given the dimensions of a Prelude.

If I were you, I'd just sell the 'Lude and buy a Civic Si (or S2K if you can afford one). You get your 6 speeds, plus a whole slew of goodies never conceiveable when our Preludes were made (LSD with VSC, drive by wire electronic throttle control, 6 disc in dash changer w/mp3 and even navigation, side and curtain airbags). All for about $21k. Great deal.