This is my personal opinion, which you don't have to agree with, but as you seem to have concerns about going forward with this, I will tell you what I think.

Take into account that stem cell transplant involves high dose chemotherapy with all its short, intermediate and long-term risks.
Also, to the best of my knowledge, up till now SCT has not been shown as a cure for any autoimmune disease (although some do achieve fairly long remissions), which means that you will quite likely still require other treatments after it.
In fact "transplant" is a bit of a misnomer, because you are getting back your own hematopoietic cells with the hope that the drastic change in your immune system (due to the high doses of chemotherapy and possibly other immune modulating agents that would not be tolerated without this rescue) will lead to cure or at least a very long remission.
In my opinion it is justified in a life-threatening or severely disabling illness for which there is no alternative treatment.
The way you describe your condition now,doesn't sound to me like this is the situation.

I am not familiar with the specific protocol they are using in this trial, so possibly they have ways to increase the benefits and decrease the risks, as compared to the standard SCT protocols, but I think that this is something you have to check.

I know this is a tough decision and it is very tempting to think that there is some "magic cure" that will enable you to be just like you were before.

I wish you the best with what you decide,

alice