You don't install the App after you move it to /system/app. Once it's there, it's technically installed. If you renamed the existing APKs, then you're not overwriting them. Move the new files over to /system/app, fix permissions and reboot, then you should be good to go.
Although, let me make sure I have this straight. You're running MIUI on your HTC EVO 4G, and you want to use the stock HTC calendar and calculator instead of what comes with MIUI? I have no personal experience with MIUI, so I'm not sure that's even possible with MIUI being an AOSP ROM not built from a stock Sense ROM. I can't think of a reason why it would not work, but I thought I'd throw it out there that your issue could be a MIUI thing.
To be honest, if my replies don't help, you're probably better off posting this in the EVO 4G forum.