I'm 32/male/healthy and have had issues with ejaculating. No pain, but very little semen is produced. I have a micropenis (3"). Could that be a factor?

Ejaculatory problems. There is no association between having a micropenis and low sperm production. If you are attempting to have a child, a detailed evaluation by a urologist is beneficial. If not but you seem concerned, do so as well. Good luck.
Yes it could. You might have sex chromosome abnormality such as klinfelter's syndrome which is associated with a small penis as well as small testicles. Could also be so called partial androgen insensitivity where your genitalia fail to respond fully to your own testosterone. Could also be a hormonal problem with low testosterone production.
Likely not. Most men who think they make very little semen make normal amounts. As low as 1.5-2 cc of semen is normal. That's as little as 1/3 of a teaspoon.