In my opinion "needs a tuneup" is what people write when the engine is comprehensively knackered. Rough running can mean anything up to and including compression failure. So I'd value that boat as if it has no outboard. If you can get it going, that's a bonus.
As far as which boat goes, YOU need to come up with your purchasing criteria and then decide which boat meets them best. Internal room sounds like it's high on your list.