It's been quite awhile since I've owned guinea pigs... But, big idea here is: if they don't get along, don't force them to live together. You could try a few things like making sure they meet on neutral ground. Putting one in the other's cage is pretty much a recipe for disaster. Piggies can be rather territorial and the newcomer will be viewed as a threat... a space invader who must be dealt with; not welcomed. You could try putting their cages near one another so they can see, smell, and hear one another without risk of injury.
No, never had luck with litter training. Didn't really try. For the most part, they went in the corners of their cages, so I'd just address the messies in those locations every day and change out their entire set-up maybe once a week (or more if they were determined to be messier).
Special treats and food -- I'm no longer up on the best staple diet (like which is the best pelleted piggie food). For the most part, the store-bought pre-packaged treats that are marketed toward gp's and their humans are not terribly good for them. You'll want to aim for fresh fruit and veggies... the kind that you'd eat.