-- Prompt the user for a custom search string
set findString to text returned of (display dialog "Enter the text to search for (including message header):" with title "Full Message Search" default answer "")

-- Prompt the user for a custom flag (1-7, -1 = remove the flag)
set customFlag to text returned of (display dialog "Enter a flag (0-6):" with title "Full Message Search" default answer "6")

tell application "Mail"
	-- Get all messages in the mailbox
	set theMessages to selection
	repeat with aMessage in theMessages
		-- Get the raw source of the message
		set messageSource to source of aMessage
		
		-- Check if the custom header is in the source (adjust the header name and value as needed)
		if messageSource contains findString then
			-- Set message flag
			set flagged status of aMessage to true -- display (true) or hide (false) flag
			set flag index of aMessage to customFlag -- set color for the flag (0-6 or -1 for none)
		end if
	end repeat
end tell