Are you talking about the brake warning light on the dash? If so it sounds like there may be a leak somewhere in the brake system, the fluid is low in the master cylinder, and or there is not enough vacuum to the power brake booster. If any brake lines were disconnected during the engine replacement the brakes would also have to be bled. Any of these would account for the warning light and excessive pedal travel. Otherwise there could be a failure or wear anywhere in the system.
Hope that helps
Monday, December 4th, 2006 AT 7:14 PM