So, the moral on this one is...always check to see the person 'helping' out did everything in the right order. It is a bit embarrassing but the problem was that they never removed the wood that was blocking up the transmission when the engine went back in and bolted in the engine mounts thus putting stress on entire driveline. This was causing the shifting into 1st issue; and the fact the transmission mounts were basically blocks of wood was causing the unusual vibration. Always check for the obvious, do not trust someone else has!