You should be able to get decent spore photos without stacking (which is, I would guess, almost impossible with hand held camera). I can see the spores fine in the closer version you sent, but I would suggest trying to get the spores against an empty background -- it often helps to gently squash the mount. Then take a bunch of photos and use photoshop (or equivalent) to select the best and arrange them on a single canvas. It helps to set the selection tool to have a diffuse edge (e.g. 10 pixels) so that there aren't cut/paste edges all over. After that it almost always helps to adjust the brightness/contrast to that the background is nearly white. People often skip this step with the result that both spores and background look unnaturally gray.

Apothecial sections are harder because they often don't lie in one plane, are often too thick, and your camera autofocus will often be trying to focus on something you're not interested in, like air bubbles or dirt particles. I don't have a good remedy for those things apart from rigging up something to hold your camera in position (I think there are some cheap commercial devices for this -- maybe someone else knows) and using manual focusing.