Ok Canadiandesi....your situation is quite tricky. Sorry for being direct... it is not going to be a good news... you will certainly meet judge if you are short of days... sad part is even if judge gives you favorable decision, it is likely that CIC will appeal against it in federal court!!!..... (please check some of the decisions in the court webpage http://decisions.fct-cf.gc.ca/fc-cf/en/d/s/index.do?col=54). Just type in 1095 days in search text and read some cases...
My first application was rejected for the same reason in 2009-10 ( I had fewer days than 1095 ... may be 975 days of physical presence since last four years of my application date, I thought i had a good reason for absent days- i was away in a foreign country collecting data for research conduced in Canadian University)... I gave the test and passed, met the CIC judge who flatly denied citizenship..... I didn't appeal and preferred to apply again. It seems that only exception for less than 1095 days is if you are sent away from the country by federal govt/or any other important agencies (like defense, foreign affairs etc... this is just a hearsay, i am not sure)
I applied again after safely completing 1095 days (with lot of buffer days) in Jan 2012. I got the oath date for next week.
So, Please be prepared for some not so good news.....I hope you get lucky....