If they are offering that kind of deal take it. I would be wondering what eles they found when they tore it apart.
Believe me they will use that offer against you if anything else happens to the bike after they fixed it and you go the lemon law route.
Remember this is business. You will find another bike, hell you said it would take 3 to 5 weeks to fix it anyway plenty of time to find another one.
Good luck.
