I usually file online with H&R Block. When I get to the part where I'm supposed to enter W-2 info, there's a little box to check in the W-2 is handwritten. I've never had to deal with that, but the presence of that box makes me think their website might have some info for you about dealing with handwritten W-2s. Or talk to an accountant, or someone who has worked at that bar for a few years, anything to avoid having to spend a few hours on the phone getting in touch with IRS people.
As for the taxes taken not jiving with what you (or she) think was taken, I'm not sure what to do besides speak to the employer. If you can't get straight answers there, you might have to grin and bear it (and pay up) since you don't have the proof of the pay stubs. Again, contact a local accountant.
For future W-2s, I know some people say to keep all of them, but I detest storing too much paper, so I don't. I keep the first and last from each job for each year, and if I have a raise, promotion, or change in status of any sort during the year, I keep the last one from before the change, and the first from after. These get dropped right into the Taxes folder in my files, to be dealt with in February (when I usually file). All the stubs in between go through the shredder. Actually, the little bit I keep seems to be overkill. All I've ever needed (so far) is the last of the year. I compare it against the W-2 to make sure the info matches, and file it away with my return.