What is the real risk of taking 400mg of ibuprofen daily for 3 years? 
I know there are kidney risks with high dosages, and very long term,
but what about 3 years at this low a dose?

It's probably a lot safer than taking 800mg doses 3x/day (max) since
you are giving body time to clear out the drug through normal
metabolism.  However, even at that dose, you are increasing chances of
developing ulcers, which are more common than kidney failures.  One
precaution you must take is to never take the drug when the body is
dehydrated--i.e., after long periods of exercise or drinking alcohol. 
TV advertisements of people taking Advil or Alleve after playing
sports for sore joints and muscles are dangerous for this reason. 
There is an added benefit of longterm ibuprofen (or other NSAIDs) use,
I believe, which is reduction in colorectal cancer incidence. 
Rheumatoid arthritis patients who have taken NSAIDs for years have
shown much lower incidence of colorectal cancers than general
population.  On the other hand, the latest findings of increase in
cardiovascular event (stroke, heart attack) with use of Vioxx will
likely apply to traditional NSAIDs as well.

There are some caveats to concluding it is safe. I took it at a higher
dose for half a year; I presume you are thinking of seeing a doctor
occasionally. When the FDA reviewed evidence that it was safe for
approving 1200 gm a day. there report at
http://www.fda.gov/ohrms/dockets/98fr/082102a.htm gave a lot of
information to consider.  The report was generally positive.  They
also said:
"In 1996, the National Kidney Foundation published a position paper 
in which it recommended that consumer labeling of OTC analgesic drug 
products contain warnings directed to the population at risk for the 
development of nephrotoxicity associated with the use of these products 
(Ref. 67). These recommendations were based on the review of a database 
that contained 556 articles on aspirin, acetaminophen, aspirin/
acetaminophen combinations, and NSAID-related renal disease by an ad 
hoc group of expert investigators and clinicians. This committee 
suggested the following consumer warning for OTC NSAID-containing 
products:
      DO NOT TAKE THIS PRODUCT WITHOUT PHYSICIAN SUPERVISION IF: (1) 
You are allergic to aspirin; (2) you are under a physician's care for 
asthma or stomach problems (such as heartburn); (3) you take diuretic 
medicine; (4) you have heart disease, high blood pressure, kidney 
disease, or liver disease; (5) you are over 65 years of age."
  They also mentioned occasional cases such as asymptomatic early
kidney failure that led to kidney failure when the person was taking
400 of ibuprofen 3 times a day.  These unusual cases of kidney failure
on low doses responded well to treatment.