With regard to the flush valve and flapper, the consensus on here seems to be that on a generic toilet, the Korky flapper is the best. Korky makes a universal flush valve that has a wider overflow riser than most, and is twist-to-lock adjustable as to height, so you don't have to cut it, and it comes with a Korky flapper, all made in usa. You can get it at Lowe's: Korky Flush Valve
Also, you can see instructions, videos, etc. at the Korky web site. www.korky.com They also happily answer questions on their phone line in Wisconsin; super-nice folks.
The consensus isn't as great re the fill valve, but on the flush valve and flapper, I think the Korky is most-recommended.