The only thing that comes to mind is the master cyl. If the return valve is sticking that is the only way i can see this getting worse with the new parts.
New caliper and disc make the brake opperate better than the old stuff so the effects of a failed master cyl will be all the more obvious.
The fluid in the brake system has to be able to move, brake fluid doesent compress which is the whole point of it so it can pass on the force of you pressing on the brake pedal. If the fluid cannot return through the master cyl then the pressure will increace in the caliper, causing the pads to drag, this causes heat, that makes the fluid expand, causes the pads to drag, causes heat. You can see where it's going. Then the release valve finally unsticks and the brake works properly.
You used the example of the bus, if you wound on the power to get past the bus that will cause the chassis, swing arm, etc, including the wheels of the bike to flex. Perfectly normal but this flexing WILL bring the pads into contact with the disk and we are back to the previous paragraph with heat causing the fluid to expand etc.
I had something similar happen on the front brakes on my suzuki where they put themselves on when i got a move on through the twisties. Replacement master cyl fixed that.
Oh and if it is the master cyl then you are entitled to ask for a refund of the unessesary parts as the 'proffesional opinion' is wrong. You may even get away with the labour for returning your bike to its original condition if your canny about it. Don't think you will be able to do much about the wheel bearings but the disc/caliper kit that was not required, thats different.
(edit) I have VERY little faith in bike dealers, the small experience i have had with ANY motor trade people who i do not know personally has always, always been a let down.