The mirc.ini you need is the one actually used by mirc. You can find it in this folder:
//echo -a $mircdir
//echo -a $mircini
The reason you couldn't find was that those were the defaults from before the program is actually used. If the mirc.ini is in the same folder where mirc.exe is located, then it uses that file. Otherwise it uses mirc.ini located in c:\users\username\appdata\roaming\mirc\mirc.ini and it will create from scratch if it doesn't exist there.
It can be hard to use windows to search for appdata if you have the setting to treat AppData as a hidden folder which should not be seen or searched into.
It sounds like it would be simpler for you to just add some dummy searches until the stuff you want to be gone doesn't appear in the dropdown list anymore.
Or you could try Raccoon's suggestion, with only a small alteration. To defend against the chance that the pathname for your mirc.ini has a space in it, you might need to put it inside quotes, like:
; first save a backup copy, that you can only use by copying back while mirc is not running:
//saveini | copy $qt($mircini) backup_mirc.ini
; To clear the CTRL+F find history in mdi windows.
//remini $qt($mircini) find2
; To clear the CTRL+F find history in script editor.
//remini $qt($mircini) find
; Optional. Just to be sure. Also type:
; after you're done, this should say both are zero:
//saveini | echo -a $ini($mircini,find2,0) $ini($mircini,find,0)