You dont run the rod all the way through when cleaning a ML. I put several gallons of HOT! water in a bucket, pull the barrel out of the stock and place the barrell nipple end down in the hot water. A patch on a cleaning jag attached to the end of your ramrod will pull water from the bucket up through the bore and when you push the rod downwards, purges the barrel of fouling. The patch acts like a piston ring and seals the jag against the bore so when you pull up it actually draws water with it, much like a syringe will pull medication out of a bottle. I flush a few strokes with the nipple in to flush it out, remove the nipple and continue flushing the bore, changing patches every 10 cycles or so until the patch comes out clean. I then change to a fresh bucket of HOT! water and continue until I feel all is clean and the patches are white. I then dry the exterior of the barrel with a rag and run dry patches down the bore. For some reason, maybe the added friction from lack of water? more residue comes out at this point, not black crud kinda light brown (Flash rust?). A few dry patches and it's gone. Blow the whole thing down with compressed air since water seems to get trapped under the barrel rib and between sights and dovetails, etc. Swab the bore with rust preventative oil of choice (I use Ballistol) wipe the barrel exterior surfaces and the barrel channel of the stock and put it back together. I run a pipe cleaner through the ignition channel and the base of the nipple, lightly oil the nippl e threads and reinstall the nipple. I like to fold a cleaning patch in 1/4's and let the hammer down on it for storage. That's how I do it. Some may have variations of it. Periodically I pull the lock, clean it and re oil and check the screws for any loose ones.
Idaho PRB