Mycobiont,
Moving from images A through E, it appears that noise is increasing. Any idea why this is? Are you increasing your ISO? Or is your histogram moving toward the left?
Plastic from most milk jugs, in my experience, is too close to transparent to be a good diffuser. To test it, try looking at a light through it; if the light is not broadly diffuse, try another material. For a very good, cheap diffuser, try a double thickness of tracing paper—you could line your milk-jug ring with it. Rik often uses facial tissue--a layer or two of this, taped loosely inside you the ring, might also work well.
This said, images with a single, diffused light source are often very sub-optimal in the macro studio. To make better use of the single flash, I’d suggest trying only bounced light from it. A neat trick for this to cut a ring from a polystyrene coffee cup, remove about a 45-degree section out of it, and place the remaining ring on the opposite side of your subject from the flash, so that your flash is pointed into the missing section. Then fold, trim, and place the scrap of polystyrene to completely block any direct flash light from hitting your subject. What you’re left with is entirely bounced light, which can be quite nice. (Also: If you like this light but want to "sculpt" its modeling a bit, you can flock inner portions of the bounce ring to subtract light here and there.)
My sense is that your lens needs to go. For a better objective, can your budget cover $100? There are some nice Nikon N Plan 10x/0.30 160/0.17 objectives on eBay for this price or less. This is a classic objective that many of us cut our teeth on, and that is capable of fully professional images. I paid $350 (second hand) for my first specimen of this lens, and was glad to get it at that. To see them being ignored now makes me shake my head. (I have a spare--PM me if you'd like to try it in your rig to see if it improves things.)
BTW, your shelf of stains and reagents makes me smile. I’ve studied lichens/fungi a bit, myself.
--Chris S.