I have other health issues that are probably to blame for this happening, but a little over 2 years on T I started menstruating irregularly. The time in between periods would be 2-6 weeks and constantly varied.
The way I was able to deal with it was by increasing my dose as it was on the lower end of normal and having a Mirena (hormonal) IUD inserted. Increasing my T did nothing while the IUD has stopped it completely. The hormonal aspect is a little off-putting, but in reality the dosing of progesterone is so small that outside of the uterus the levels of progesterone are negligible. I no longer menstruate and don't have to resort to a hysterectomy.
The only issues I've had are cramping the day after my shot, and no one knows exactly why that happens but it is well observed in trans men, and very light spotting. The cramping has gotten better over time and I expect it to go away eventually (as it does for most people). Note that a history of painful menstrual cramps makes this more likely to be bothersome and increases the likelihood of pain when it's being inserted. I'm not gonna lie, it hurt a lot going in, but I'd still think it's worth it if it were more painful.