Those thoughts do come up from time to time, but their frequency decreases with being longer on the HRT. Maybe You should consider taking some minor antidepressants to cope with, because transition - if taken on a day by day basis - is quite exhausting both mentally and physically. It might seem that it is all roses and butterflies, but there are nasty things and thoughs which do creep in at times, and then You get over them and forget until something else happens... Also, when people post their experiences they tend to do that in encouraging manner which is nice and commending, of course, but sometimes can cause wrong perceptions and assumptions. Your transition will be Yours only, it is Your unique and personal experience, I wish You that Yours is smooth and without issues, but please be prepared to deal with rough parts of it.