Follow along with the video below to see how to install our site as a web app on your home screen.
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Use root explorer
copy /system/app/Mms.apk to your sdcard as a backup, pop the new one in there. set the correct permissions (you can see them in details on the original if you longpress it)
Then just overwrite it, and wait a little while or reboot.
don't try to actually install the apk.
Just out of curiosity, did the new one show up in your app drawer or anything? From what I can tell, apk files seem to be mostly hardware independent as they run in the dalvik vm. It's like a java applet. If you didn't, it was most likely the permission weren't set to the same as the permissions that other apk's have inside that same folder.