electric fault with car?

here i find myself totally baffled, i have a peugeot 206 1.9 diesel which has recently had a new engine fitted, everythinng is running perfectly, charging fine etc.
the problem is that the battery light is coming on very faintly when started. It doesn't come on at all when the car is primed to start and when the interior light is set to the on position whilst the engine is running the light comes on fully. I am wondering if this would have anything to do with the stereo electrics as it didnt have one in it when i bought the car and all the connectors had been cut off, does the stereo act sort of like a junction box for any other electrics, ie interior light?? Also the car has to be revved up before the clock display will come on amd the headlights brighten slightly also as if it is building up resestance somewhere, i dont know much about electrics mainly mechanical and it has the classic 206 fault where the central locking doesnt lock with the fob but will lock with the door and unlocks with the fob fine, any ideas to what it could be would be greatly appreciated