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1) At the moment, the way to do this is to pull up the "armor" sheet and see which have higher scores and which have lower scores. We're working on UI improvements for this; we're currently a planning a "largest upgrades from instance X" table - i.e. a list of the largest upgrades available in Karazhan, or in Heroics, or in SSC - or whatever. In terms of differences within a particular slot - it would be straightforward to add a column to the armor sheet that would give the difference between a piece of equipment and your current gear - do people think this would be helpful?
2) Expected DPS is sort of buried in the sheet right now - if you look at the end of column B on the sword or dagger sheet (as appropriate), you will find a dps number. Since this was initially designed as a gear comparison tool rather than an explicit dps calculator, I didn't initially worry about making it particularly user-accessible. However, again, if it's a feature people think is helpful, it's not a hard feature to add to display that dps number in a more prominent location.
3) The offense values are in Effective AP. The defense values are in Effective Stamina. The total column is a weighted sum of the two (speficially, offense + .6 * defense).
And as a general update on progress: we're almost ready to release 0.4; we've been held up by some compatability issues between Excel and OpenOffice, but are getting close to a completed revision, which will include, among other things, the improved UI, full socketing support, the new test realm items, and an updated of Warp Spring Coil to reflect the recent change to it on test.
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