now theres a challenge.
Hard to say how feasible it would have been without seeing your model, but i think a lot of your problems could have been solved with some constructive grouping.
As for the circles not lining up, if you make sure you always line your circles up to the same point in your model and always use the same number of sides you shouldnt have too many problems. The thing to remember here is that all geometry in SU is made from straight lines, so with your circle youve got to make sure all the lines match up.
A cleaning tool would be very useful, although i believe there are a few rubies that already do some of that.
A healing tool could be pretty dangerous in the wrong hands. I've got images of shoddy house models with thousands of healed faces everywhere...
And lastly, the zoom issue is a known problem called clipping. I think its something to do with openGL, although im very rough on the specifics.