Cannot restore from Time Machine Help Please

HI

Using Mountain Lion , fully updated , however had a Problem with Internet , stopped and could not get it working , so was time to do a Clean Install - first time ever in 5 years since new so probably needed it .

Anyway I have done a Clean Install of Mountain Lion - erased disc first , just trying to restore to a good stage , have restore all Files/docs/pictures/music/etc just by copying over from External HDD ,
But have lots and lots of Apps and games , many I have fresh downloaded , or re-installed from the DMG i have kept , but there are some APP's and Games i want back that i cannot find anywhere else , Plus games have saved stages and things like that -

Every time I try to restore a Game/App i get a message ""The operation can’t be completed because you don’t have permission to access (name of App/game)""
I go into Time Machine find the correct one and Click restore on the right Hand side ?

So can someone tell me what has gone wrong and how to Fix , Obviously the permissions are wrong (have done a Fix permissions on Computer HDD - do not have option to do on TM hdd though) , could this be as maybe a new account when set up the mountain Lion again ?

Also is it possible to restore a App in it's complete form , with all settings and bits Via time machine as I also have Mac mail before working with Hotmail using a mboxmail system that i cannot get working again either so a restore of that would be great also.

Thanks in Advance all
Mark