A few things.
Do be aware that the depth-of-focus at the negative is much shallower than at the easel. I can tilt my easel severely to correct perspective and still retain good focus, but a misalignment of the negative stage or a severely curled/popped negative will show soft areas even at rather small apertures.
If you're printing at a wide aperture to "soften" the grain, you're likely softening everything else as well!
Heat absorbing glass (or anything, filters, etc.) that go between the light source and the negative will not affect sharpness as long as they are not too close to the negative (i.e., sitting right on top of it).
For smaller prints, smaller apertures are usually alright. The slight bit of degradation due to diffraction from the smaller aperture is usually too small to be resolved at small magnifications. In other words, you can ignore diffraction till you start making larger prints, and then you'll need a larger aperture anyway.
Negative "popping" doesn't always deform a negative; sometimes, especially if the negative is sagging a bit in the carrier, it actually straightens things out a bit. Still, it's better to get the neg as flat as possible in the carrier and avoid popping by keeping the negative cool, one way or the other.
Best,
Doremus