Refactoring: Biting off more than you can chew?

So as most can assert from reading my blog I have developed a stamp tracking software "suite" of tools. The core of this was based off a JPA implementation which was recently moved to EclipseLink. With some of the new tools available to Eclipse for use with JPA (in particular Dali), I decided to think about reorganizing my services and trying to streamline some of my code (Using MappedSuperClasses as abstract parents for example). I focussed on my StampModel module which had a pretty decent unit test coverage of around 80% (some of the code not covered include error handling and a lot of my upgrade code) and was also where all of my entities existed. I even created a bugzilla entry for this work so that I could track my progress. I estimated it would take me no more than 12 hours. Well, 30+ hours later I finally have repackaged, rewritten or revamped the module (and database tables). For the first time in nearly a week I was able to open my Swing based editor last night and manage my collection. I still have some outstanding issues, but my refactoring is pretty much complete. There are a couple of lessons I took away from this.

1. Never assume how long it will take. Invariably something will come up (and I have to admit the Olympics coverage may have pulled my attention away from eclipse on occasion).
2. When I started refactoring I relied on my unit tests and decided to make updates to the Swing client after refactoring was completed. This was a mistake as often I had to think back to what the update was rather than making the change immediately (I am thinking along the lines of repackaging, changing initialization code etc.) Overall these changes tended to be pretty simplistic (change package X to package Y) but occasionally a DAO that I did not particularly like in the previous module was changed. In one occasion, the new DAO did not really fit and I had to rewrite some controller code (but at least it is better now).
3. Part of my refactoring was to move my entities which were annotated to be orm.xml based. I should have done this first without changing the data-model. Changing the database schema along with moving the entities to orm.xml created a lot of thrashing to work through.