Zach,
Just because the flow is slower doesn't really mean that the coffee filters are working to reduce yuckies... they would be slowing the flow of the water into the pump and eliminating silt, tiny gravel, etc from entering the pre filter. The main filter is sufficient for most anywhere in the US. I haven't heard of any US water bad enough to contain viruses.

Coffee filters are a nice item to include to use as a scrub pad, pre-filter and firestarter. There's a multiuse item for you!

The glass-fiber element will clog when used with silty water. It's happened to me with a large group and all 4 filters clogged. I say this to let you know that any type of pre-filter is a good prefilter. Yes, it may constrict the flow of water, but it will help prolong the life of the filter.

Concerning the original post:
If you are able, it may be a good idea to collect some water into a bowl/pot and filter out of that. This allows the silt to settle a bit and you can get a cleaner pump. Pumps clog, filter fail. You just have to make the best use out of what you have.