I think it was the gen 4 auto boxes that tend to be a bit weak... I could be wrong though!
Although generally just the usual stuff; service history, rear arch rust, cambelt etc.
I think for what it's worth, you may as well get the petrol... There's only about a 10mpg difference, considering the price difference from petrol to diesel, would you be saving that much in fuel?
I think all cars have their horror stories, so I wouldn't take all bad stories that seriously.
A looked after legacy will go on forever!