Well, allow me to post a few observations in regard to these resizing issues, that I made before that ultra-easy way to convert units actually became reality (I wasn't that smart to discover it in one day and how it is written in the manual wasn't at all alike my first converting work when I just started...)
First of all the resizing problem: don't think too easily of it! Basically in most cases any resizing of the actual graphic will FAIL. This is simply because every unit has an assigned amount of pixels, as has every frame. Once you change the size you change the amount of pixels, therefor merging some of these, thereby often moving them with 1 pixel in one of the 4 possible directions. From own experience I can tell you that this will always mess up the whole animation (I call it the fever-effect, I guess you can imagine something by it and it does NOT look nice in the game). The only 'safe' way to resize stuff is enlarging the graphics, but that won't be usually what you wish...
Second: the resizing of the frame (i.e. to remove the 'dead space', without actually resizing the graphic). This is as such easier to do as that if you don't screw it up yourself the success is sort of 'guaranteed'. This was also how I actually converted the first units, before I discovered the full usability of FLICster - simply by cutting-out and pasting the parts from a converted cardboard which is the standard option of conversion in FLICster. In that way you can get the right frame that you wish. However, there are certain drawbacks:
-It requires a lot of calculations and good preparation. All frames have to be not only exactly the same size but also the unit-graphic needs to be all the time relatively in the same place, which is not that easy if you use a standard imaging-program only. Especially the placement of vertical cuts is tough as you miss good reference points in the images, especially for moving units. And if you make only one mistake - either by cutting or pasting the frame, the whole animation is screwed, and fixing it is not that easy at all...
I worked eventually myself with a calculator by had, counting and writing down the pixel positions to get the proper cuts... in that way converting only 1 of the 11 required animations took already half an hour.
-Besides the sole issue of lot of precise working you might also soon find out that such resized graphics simply get screwed up in game - apparently the eu-engine is not able to work with every possible frame-size and/or with the total size of the eventual animation. So you have to stick only to sizes which the game can handle and here I cannot help - I made some calculations myself while working (I designed myself eventually 1 sole size that I used for all units - it did sort of made the whole calculation-process easier as well btw ) but I don't have my notes anymore so the eager to experiment is all alone to rediscover it...