Bill,
Start with the brake light switch under the dash. Its a white box on the 2002. How far do you have to move the pedal before the lights come on? If not very far, I would replace the switch. There is no adjustment for the switch after the initial installation according to the service manual. But see if the switch housing is tight against the mounting bracket. If it looks like the plunger on the switch can go in further, wrap some electrical tape or glue a shim on the tab attached to the brake pedal so it pushes the plunger in further.
I don't think what you have done to the tail lights is an issue, the power source for the brake lights is under the dash.
Good luck
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John & Terry 
"His" - 2002 Inferno Red Touring Edition
"Hers" - 2003 Electric Blue Limited Edition
Del Val PT Cruisers
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