Mail.app running off desktop after installing Lion 10.7

I installed OS 10.7 Lion on my MBP 2.33 (2007) a couple of weeks ago. After installation Mail.app wouldn't launch. Mail would be present in the tool/information bar at the top of the screen but wouldn't load the UI at all. I tried several things including force deleting the Mail.app (using App Delete) and all the files from the ~Library folder then reinstalling it from the Lion Options folder on the OS Lion thumbdrive but I got an error notice saying:
You can’t use this version of Mail with this version of Mac OS X: "You have Mail version 5.2 (1278/1283). It can’t be used on Mac OS X Version 10.7.5 (Build 11G63b). For more information, click the Help button."
Of course help was no help. [I found it odd that the mail version that came with the OS wasn't compatable--but that's a side note.] So I went on some of the forums and found out that if I took my last working version of mail from my clone/backup (in this case my clone of Snow Lepard) and installed it on my desktop it should work (I also replaced the files I deleted in the ~Library folder too). IT WORKED!
My problem is that I want to put the program back in the applications folder but the "old" version still resides there and it wont let me move or delete it giving me this message:
“Mail.app” can’t be modified or deleted because it’s required by Mac OS X.
I'm a little more hesitant to force delete it like I did before because I dont want to jepordize the Mail.app that is working.
So now I have 2 versions of mail on my computer #1 in my applications folder that doesn't work and #2 on my desktop that does work.
My question: HOW DO I GET RID OF #1 AND REPLACE IT WITH #2?

Many thanks to everyone above !!
What a super, super pain. I upgraded from 10.8.3 to 10.8.4 and the MBP (MacBookPro4,1) would not start, except in Safe Mode. I tried downloading the update from Apple - didn't help. I tried the Combo update - didn't help. Couldn't find anything on the discussion boards, except that it was a problem with the graphic drivers.
Finally decided to do what lgiraldin did - wiped the HD, installed 10.6.3 from my origional DVD, migrated my data from the copy of 10.8.4 I had made, the upgraded to 10.7. Everything seems to be inplace except Mail would crash. Re-installed 10.7.5 from the recovery disk but it didn't help. Replacing MAIL with Pacifist didn't help.
I also found that my timemachine backup could not be used for recovery as it is on an Iomega network drive - the recovery partition does not allow me to mount the Iomega.
I found an installation of 10.7.5 that I had on another disk. Booted from that, copied the folder to the MacBook Pro HD, and now mail opens and runs correctly. Better than 10.8.3 too. In 10.8.3 it would often take 100% cpu and lock the entire computer for 1 or 2 seconds.
Thanks to Terry Mahoney and ApplesDownfall especially as I didn't have to wipe and re-install everything a THIRD time. I've wasted most of three days because there was no way to back out the update. Now I know that I have to create a Carbon Copy clone of my HD before any update. I'm going to stick with 10.7 until **** freezes over!

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If it asks for your password, type it in and hit return.
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