Well, for starters there is the "johnny cochran" issue: not legal to modify an appliance like that. You violate it's GAMA/AGA/UL listing, and hence lose the permit it was installed on.
Aside from that, now you don't have the air flow balanced against the heat produced. That can't work out well. \
And most important, you affect the operation of safety circuits like hi temp limit switches, etc. Those were all designed around a certain burner/fan operating scenario, and now...who knows.
If you don't need 100,000 BTU, a whole new furnace is not that expensive, and if you want uber energy efficiency, you get a new furnace which is DESIGNED to operate the burners in stages, and modulate the air flow accordingly. The unit costs more, but in a very cold climate can save a lot of energy. If you are upstate like in Buffalo or something, this would be worth doing.
Messing with a furnace on your own is a bad idea.