Will marinating beef in baking soda + water mixture for long ruin it? I have some tough meat on my hand, what should I do for stir fry?

I would suggest adding some acid as well, since it has wonderful tenderizing properties. Vinegar or lime juice would also add a nice flavor component.

I've never noticed any advantage to leaving the meat sit more than 15-20 minutes, but I recall reading the folks at Cooks Illustrated did. I don't think they said it was really detrimental for times up to about an hour- but I don't remember if they opted to go longer. There just wasn't any particular advantage to doing it longer. One thing that might help, in addition to the marinade is to cut the meat very thinly on the bias. That gives you shorter muscle fibers, which is why corned beef and brisket is sliced that way, and that lessens the chew factor. I'd also recommend taking care not to over cook the meat either, even if that means leaving it a bit on the rarer side than you would ordinarily. Your other option might be to chop it finely in the food processor, and use it as you would minced pork or chicken.