Applying to Ph.D. programs: Should I include my master's degree transcript?
You do need to include your Master's transcripts when applying for a PhD.
Aside from the academic dishonesty issue of not including your transcripts, having taken many of the core courses at the graduate level will make you a more attractive candidate, as they will know that you do not need to take remedial coursework before beginning doctoral-level studies.  Having the Masters will also make it a lot easier to get teaching assistantships, since those often go first to those who already have Master's degrees.  Your letters of recommendation, too, need to come from academic references for your PhD (not supervisors or coworkers or general character references), so you will need to get letters from your Master's degree professors that can speak to your potential/experience as both a researcher and as a graduate student.  So I would say a definitive yes to including the transcripts.

The second question you need to consider is about whether to address extenuating circumstances in your application.  I think it is helpful to address, but only insofar as it presents you in a more positive light; that your disability helps you to better understand the situations that your students face, that your health issues have helped to build your resilience so that you'll be capable of long term study and research, etc...  This might be especially important to include if you have obvious "red flags" on your transcript like withdraws or incompletes - so that they both know there's extenuating circumstances but also know that those same circumstances are not going to wash you out of the doctorate.  (Which is why you'd always want to portray those circumstances as an asset rather than a liability). So this one is a little more complicated and will require a lot of thought to deal with in your application statements.