Thanks, Phil. This tells me what I needed to know about the cropping.
I'm fairly sure that the softness in your picture #1 is due to diffraction. Very small apertures are guaranteed to do that, and once your aperture gets small enough to see the effect, it gets worse in direct proportion to the f-number. You can compensate quite a bit for that softness by sharpening in post-processing. I do that routinely. For example the
aphid predators that I just posted, got sharpened by Photoshop unsharp mask at about 70% with 1 pixel radius (working on the camera resolution images).
I'm not so concerned about the long exposure time as Mike is, but it is something to think about. If your setup is dead stable, then you can expose as long as you like. Before I got my nice bright halogen illuminator, I routinely used several second exposure times with small apertures and basic photoflood lighting. But if there's any vibration, the image can get a little fuzzy, and if you're really unlucky, certain patterns of vibration can look just like diffraction blur! (I know this, of course, because it's happened to me.

)
Again, I recommend to run test sequences isolating each aspect as much as possible. Make sure there's no vibration, set up the lighting and don't touch it, and run a sequence stepping aperture from wide open to full closed, adjusting exposure time to keep the image brightness constant.
You ought to get a sequence like what's summarized at
http://www.janrik.net/insects/ExtendedD ... deoff.html. Chances are that full open will be fuzzy from aberrations, someplace around f/8 will be as sharp as it gets, and from there down the images will first lose sharpness and then get frankly fuzzy.
Once you do that, you'll have a good start on understanding the effect of aperture.
Then you can start to work on lighting, which is an art form of its own!
Hang in there -- you're doing fine!
--Rik