Could it be a misfire? You could try checking the spark plugs to make sure there's no coolant on them and that they're not fouled out. You could also try disconnecting and grounding individual spark plugs to isolate if there's a cylinder that's contributing less. Since it's not as bad when it warms up (air/fuel is easier to light when it's heated up) that's why it sounds like a misfire.
If you check the plugs you might as well do a compression test to make sure you didn't blow anything. How old are the plugs and wires?
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2005 Suzuki Hayabusa GSX1300-R
1980 Ford Thunderbird - 255 V8
ported heads, 5.0L ported stock headers, O.R. H-pipe and Flowmaster 2-chambers, dual roller timing chain
hi-po Mack Truck hood emblem 
1985 Mustang GT 5.0L T5, F-303, GT40p, headers, off-road h, flowmasters, MSD stuff, etc.
Sold 02/06/04 
1989 Mustang GT ET: 13.304@102.29 mph (5-24-03)
Sold - 1998 Mustang Cobra coupe, 1/4 mile - street tires: 13.843@103.41 (bone stock)
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