Two suggestions here for the price of one. Bargain.
During the bulk upload process, would it be possible to have a log generated for the Stage 2 portion of the upload. Nothing is more annoying when removing a selection of out of stock items than seeing 10 items were closed, 2 items were not closed. Then you have to go through the whole process manually to find the two still open items. A log file with a list of items closed or otherwise would be exceptionally usefull.
When doing a bulk upload, is there any chance that the "overwrite" option could also have the facility to use the SKU as its comparison field. Again, it's a similar situation as above. You correct a typo in your master database, or change the title to something more informative and you've got suddenly got an addition rather than an overwrite. Then with no stage 2 log you have to manually figure out which one has gone wrong.