John, I'm afraid that any comfort I have to offer you is so small compared to the enormity of your loss, but as someone who very nearly left my loved ones in the same crying city of the dead because of my own silent struggles with depression, I offer you something I think your son would want you to know if only he could tell you now.
Depression is a disease that is no one's fault, it is like cancer in many ways because it takes too many wonderful lives and cuts them short, and losing even one is one too many, so we struggle to keep each other alive, to recover, and to avoid relapses. Transgender youth are especially prone to depression, not because of anything wrong with them or with their families, but because of how cruel this world is to those who are different, and how cruel the internalized rejection with which we can reject ourselves because we aren't 'really real'. No one can know why some of us who suffer will eventually succumb, why our strength will reach a crisis that we can't overcome. So we and the people who love us do all we can and hope it will always be enough.
When a wonderful child fights a long fight against cancer, and eventually has a sudden complication they couldn't overcome, we mourn, but we take comfort in the belief that the support we gave them and the help from medical professionals they received, together extended their lives many months or years beyond what it would have been if we had done nothing and they had not gotten the help they needed.
With suicide it is the same truth. Your loved one might have died many years ago, and you would never have gotten to know the good years you shared, if they hadn't have gotten every bit of the love and support you gave, and the treatments they received to enable them to live with their gender dysphoria and the terrible depressions it can create or exacerbate.
I wish with all my heart that your son would be here still now in the city of the living where you raised and loved him. But please know, he and you didn't ever have a choice to pick the challenges he would face or the odds stacked against him. From what you have said, you all did a wonderful, even heroic job, of being there for him. Thank you. Thank you for giving him a better life, and a much longer life, than he would otherwise have had if he didn't have all that you gave him. May their be more parents and families like you. And may you come to know that he is with you still, because he is loved and will always be.