AFAIK Grady doesn't recommend the 300s on the older boats. My impression from reading is that has some to do with transom strength, as well as some to do with overall hull structure. My 2002 has a factory refit where they added new foam stringers in at the forward edge of the aft cabin- I think it was here that I read that the early boats were designed to be lightweight since the power options in 2002 were limited. My 2002 also has large aluminum bracing from the transom to the stringers - I assume that was factory original although some boat manufacturers offered retrofit kits, and there's nothing to say that a 2006 wouldn't have stronger, larger bracing.
All that said, lots of people have repowered the early boats with 300s and I don't think I've read of any issues directly related to that. Both Suzuki and Yamaha have motors that are technically 250s but same block etc as their 300 counterparts. As always, do your homework and choose what you are comfortable with.
I would not worry about the low hour motors. A lot of guys either repower to sell, or repower and then realize that they still aren't using the boat as much as they'd like.
That sounds like a decent price to me if the boat is in good shape - those motors were probably low $40s/high $50s installed.