Once the engine comes out of a bike the bill adds up quickly... Worse case scenario for the "06" is a full engine rebuild. That'll run you about $300 for crank, $50 for main bearings and seals, $200 for a replate (assuming its nikisil) and $150 or so for the top end kit. It'll probably need swing arm bearings, like most older bikes need as soon as the motor comes out, so there's another $50. So your already in it about $750 (that's an estimate, but you get the picture) just to get the motor taken care of. Now you'll still be needing all those other things mentioned above. So, if you could sell the bike for $1,200, you'd need to buy it for about $300 to just make a $150 profit. I don't know if that would be worth it to you, but that seems like a LOT of work, case splitting, bearing pressing, etc, for just $150.
As for the 98, that might be worth it seeing as it at least runs. Some minor carb adjustments, and gallons of elbow grease to get it to look alright and you should be able to flip it for a nice chunk of money (that could go to the '99!)
Projects are fun, but if your looking to make a profit, blown motors SUCK. Unless your doing a motor swap project. My numbers could be wrong up there, and someone more experienced could point that out, but no matter what you decide, good luck with em and make a build thread if you pick em up