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I'd say just keep them as MPEG2. No point really in recompressing them to something smaller as the source is really noisy, and you will end up losing details. Storage is cheap, and you can re-author them as blurays if you want, as MPEG2 is an accepted medium for bluray, and then you will have scratch proof discs that you will never have to worry about being wrecked, for the mere cost of like $15. You may want to make backup copies of the menus just so you have everything, if you are a completist haha. Old anime is very difficult to encode properly.
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