Pax, Since the basecamp is just gravity feed, did you ever try putting a clogged BC filter in your hiker after it quit? I'm thinking the pump pressure from the hiker might extend the mileage of a filter.

Terrapin,
I've picked up giardia twice, once in the Q once in BWCAW.  Near as I can tell, the first was from swimming in Shade Lake near a much used campsite and the second was probably cross contamination from an inexperienced friend not using a filter properly.  Not much fun either time.

Regarding the rest.  I used the Hiker for years until mine cracked last year (it cracked along the pump cylinder and created the best squirt gun I've ever used).  I bought a new one, thinking that my old one had lasted about 7 years of hard use.  My new one, with more fancy bells and whistles (mostly the hose connectors) actually cracked in almost the same place within about two weeks of use.  When I inspected it, I discovered that the new model is cast as two pieces and (presumably) epoxied together.  The seam actually runs along the pump cylinder and, apparently, the pressure forced a split in the seam.  I returned that one and picked up and MSR ceramic filter pump.  My friends have used them for years, but mine seemed to require filter maintenance after every liter and drove me nuts.  I picked up a Basecamp for a 12 day trip with a friend.  We liked it, but it did slow down by the end of the trip (it would take an hour or more to filter 92 oz).  I use collapsible Kanteens from REI (92 oz) to filter into and they work pretty well.  They stand up okay on their own, but I usually brace them with a rock or against a tree, etc.  I will use it again in the future, but I will always carry a hand pump, as well, to use during long days or for a quick liter or two.
GP

I'm thinking giardia takes about 10 days to kick in. So usually you're home by then. There's other things that can loosen you up too. Just the change of water or greasy meals...
Giardia you'll have the little bugs doing laps in your intestine between the sudden urges. It's pretty definite you have something. But count back 10 days if you want to figure out what happened and where you were.

This year we started hanging the base camp and letting it rest for 30 minutes to let whatever sediment settle, before opening the line.  This seemed to help.  The bag tends to sag down around the filter housing, creating a low spot for sediment to keep it away from the filter.  Usually there isn't much, as we usually fill it well away from shore.

Also, be careful to not let the water level get below the filter when filtering - you'll get air in the filter and this will slow down the gravity feed badly.  Not a problem with a hand pump, but definitely is for the bag.