Betrand Russell's
History Of Western Philosophy is a great read due to the huge range that it covers. You get to read the history of philosophy in the words of a great writer who is also a very influencial philosopher himself. Goes all the way from the pre-Socratic philophers of ancient Greece, right up to the mid 20th Century (Russell's time).
One complaint is that due to it's
massive scope much is glossed over (by neccessity). But if you would like to get an overview of philosophy before you start reading the primary sources, I would reccommend it. It will also help you to have read a book like this before you read the primary texts, as it will mean that you will be able to put the work in context, and understand its influence and its influences (none of which are likely to be obvious just from reading the texts themselves).
Also, since you are coming from a background of science and appear to be interested in the contrast between science and philosophy you would probably be interested in the Philosophy of Science - the two major works that
need to be read are
The Logic Of Scientific Discovery by Karl Popper and
The Structure Of Scientific Revolutions by Thomas Kuhn.
Make sure to get revised edition of Kuhn's book (third edition), as there is much clarification to be made by him in the appendices. Also, Kuhn is an author that
has to be read first hand. 90% of what is written about 'what Kuhn says' is total nonsense.
A great 'non-primary text'(?) for the philosophy of science is
What's This Thing Called Science? by A. F. Chalmers.
Finally -
every major philosophical work read in two years? That's a lot of reading! You could take pretty much any one of the many philosophical problems and very easily spend two years reading about it! But hell - there's nothing wrong with being ambitious!
EDIT: also, maybe you would like to provide us with your current reading list that you have compiled so far. This will stop others reccommending a book that you already have - plus it would be an interesting resource for other TFPers.