Congratulations on having a client willing to pay you for fixing an "error" as they perceive it. I have trouble getting paid for work that was done right the first time.
I am a little confused about what you are saying. As long as you keep each phone line and each leg of an Ethernet connection on a single twisted pair, it should work. If you have split pairs, then you may have signal attenuation problems. Also if you did cross over the orange and green pair, most modern equipment will auto-sense that and still make the connection. So why wouldn't the computers work?
I have never seen a computer patch cable that was wired 568A at both ends, but it would still work. I would suspect that such a cable is not a computer patch cable but a telephone line cord which is not made with twisted pairs. These may not work with computers.
