Overall it took about 3 weeks on and off between working on many other projects. FireFox's Debugging tools was a life saver but getting it all to work on IE6 as well as IE7 probably took the most time. IE7 had an issue where the OnReady wasn't called properly that took forever to debug. :/
I like how you put it all together.
One thing that did bother me just a little was the fact that the whole page reloaded after uploading file(s). See if you can just refresh the grid/tree to show the file without re-loading the page.