You get more torque from having a longer stroke in the engine and you get more BHP from having a wider bore. To get more of one you have to sacrifice the other. High BHP engines generally have higher reving engines due to having shorter, wider pistons. They have less travel up and down so produce lots of power at high revs, but when the engne isn't spinning don't do a lot. I believe this is refered to as being over square.
The opposite is a long stroke engine. Under detonation the rear wheel is under force for a longer period, due to valve timings being longer and holding the pressure in longer. However, they don't rev as high due to the longer piston travel. Typically twins are long stroke and 4's are short stroke. Ultimatly the middle ground is a sqaure triple, giving what Triumph feel is the best of both worlds. (I think they actually use a long'ish stroke triple for the 675.)
To give the ZXR400 engine more torque you would need to change the piston stroke. Adjusting the crank pivot position isn't an option without making a new crank case, but you might be able to change the piston rods to longer ones and extend the barrel length with an additional section and another gasget. You'd end up with say a 430cc engine with maybe a slight drop in maximum rpm (down to 12k revs fo safety reasons) but torque might be up by 15%.
I love my book shelf.

Occupation: Nerd (IT), and all round do-gooder. Intersts: Public displays of indecency, oh yeah... and motorcycles. Currently have a 1994 ZXR400 & a 1998 YZF-R1.
And remember...Public ignorance is a government's best friend...!