Most of the films I get are REALLY dirty! The first pass through the cleaner usually loads the pads with dirt. I rewind them and 'swap' them for the second pass. (Putting the bottom one on top and the top one on the bottom puts the 'clean' (cleanER) side to the film. After the second pass, the media is dirty again. When this happens the film stops geting clean.
What I want to know is how soon can you put in a new, clean, freshly soaked set of media pads and still not be putting on "too much - too fast"?

Don't bother reversing the pads, you won't want to put the pads that used to clean the base against the emulsion. No bother worrying about when the pads get loaded with dirt, they won't scratch...and they will still clean. If I were to show you how dirty I've ran some of my pads you would probably faint. 
I'm assuming you're at a sub run house. If so, it's safe to run a set of pads for a couple of shows and then "start the week" with a new set. That first set will pull the majority of dirt off from a few cleanings and then you can start relatively fresh at that point. For example, use a new set for your Thursday night screening and Friday. Then load new pads for Saturday through the rest of the week. Once the emulsion has hardened from use at first run theatres, it is fine.
But seriously, don't worry about those dirty pads...they won't scratch.
At the college, the prints are just crappy. We only show them to the public once. I usually screen them twice because they are sometimes in such bad shape. That way you can me sure you got all the bad splices and busted-out sprockets, etc. I get paid a lot more at the college, so I put more time and effort into the small details. Furthermore, that kind of audience is a lot more 'discriminating'. When I build up a print there are little piles of grey, dusty crap on the top of my (Potts) make up table from the film. The rollers all have little rings of grey fuzz around them when I'm done.
FilmGuard makes a WORLD of difference, even though I run the film only a few times!
After the first screening there are sometimes little gobs of junk on the pads. The reason I swapped them is because of the gobs. If I swap the pads, even though they were used, the OHTER side of the cloth is clean becasue it never touched the film. (I've been using the A-side for the screenings and the B-side for the show.) Next film doesn't look too bad. I'll do it your way and see. Maybe I'm just imagining that swapping the pads works. (It wouldn't be the first time!
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No matter what, FG is worth it. Just think, before FG, all that GRUNGE was going INTO my projector! Now, my projector almost seems to clean itself!
Note: if the print is going to be run at a changeover house and shipped immediately after the run on 2000' reels, simply pull out that worthless solid yellow or white opaque tape and build up your print leaders and all...using the opaque tape to join the leaders together. This is the only truly good use I've found for this tape. That way, the leaders do not need to be removed and the film can be broken back down to 2000' reels extremely quickly.
Collector's prints, simply run it whenever the print gets run. When the collector first gets a new print for the collection, run it many times through the cleaner (to make it look nice) and then clean it as it is being projected in the future. Most collectors probably pull out each film at least once every year or so, and that is fine. The FilmGuard will not migrate to the bottom edge of the roll or anything odd like that.
No one makes media cleaners for 16mm, but if you look in the Pic Warehouse at "16mm on a platter", you will see a 70mm cleaner that was going to be thrown out I converted to 16mm. All it takes is a couple of screws and nuts from the hardware store. 

We use the make-up table as a rewind bench. We're poor! 
I'm sure we're putting FG to the 'acid test', here but even under these conditions the stuff works.
I'm sure you guys have seen far worse prints than I have but I'm used to getting 'virgin' prints. What I get at the College is terrible by comparison.
My old IB prints have never looked better. The base scratches are gone, and the projector noise is noticably quieter.
If I had a telecine, this would be the time to transfer things.
I'm not a pirate, just a collector, just in case the MPAA is lurking...
I am going to dig out a 1945 16 print of a 1939 movie that I have that went through a theater fire in the 1950's. It is covered with base scratches, and is slightly warped, without vinegar. I think this will help it. Before I clean it, does anybody have any suggestions, besides garbage? Its an old PRC title.
The first time through, it wets the film and the second time evens out the layer of liquid. Each successive run takes off another "layer" of dirt. That's why FG SEEMED to stop working. It takes about 1/2 dozen runs to see the 'real' effect.
I tried it out on "Runaway Bride" and "6th Sense". Those prints have had over 300 runs on them. After two days of FilmGuarding them, they almost look like they were fresh out of the can! My next 'acid test' is going to be "Mystery Alaska" and "3 Kings"! Those movies have a lot of bright/white scenes and show the dirt like crazy!