That is backwards Doug... in general.. if you want more low end and less top end... you lengthen the header pipe.
And conversely... if you want more top end and less low end... you shorten the header pipe.
However Rasta... Yes ... I am afraid that a tuned pipe will usually take away some low end and give more top end.. so what happened to you is kind of normal.
The only way to get some of that back without altering the pipe will be to raise the compression... you can do that by removing the head gasket (if you have one)... or by shaving the head some.
If you want to do that... you need to let somebody with a lathe or mill to do it (dirt bike shops usually can do it... or tell you who can)... look closely at how close the piston comes to the head... and make sure not to remove too much (maybe .030").
Raising the compression might require different ignition timing... or a cooler spark plug... because the engine will run hotter.
Always check the plug color again if you make another change.