Hi there KnittyKnotty,
I'm so sorry you are having such a hard time. It's awful and unfortunately only all too common.
Here is what I have gleaned from lots of reading on this subject, and I'm sure others will be along with sensible advice. This forum is a life-saver.
Basically as you probably know what is happening is because the tissues are starved of estrogen; this will take a while to redress. It is good that you have gone back on HRT. The VA - these days often called "Genito Urinary Syndrome of Menopause" because it affects both systems - can take a good while to get better, even after you start with systemic HRT. Also, you may need to play around with different HRTs a bit, til you find which one works best for you, but you probably know that already, as you went into menopause so early. The systemic HRT will help the VA, but it could take a while.
In addition to the systemic HRT it is usually essential to do something local, which you are doing. Vagifem will only help the tissues inside the vagina, and often is not enough for the outside bits and for the urethra, so you get cystitis or feel like you have cystitis and because these outside bits and the urethra aren't getting enough estrogen you can also get slight bleeding and miscrocopic blood in the urine. Once the walls of the urethra start getting enough estrogen, cystitis will be a thing of the past.
When you switched from Vagifem to Estriol, did you use Estriol every night at first and then reduce it gradually? Are you using it both on outside as well as on the inside ?
I was told by my specialist to try Vagifem inside, as often as 5 nights or even 7 nights a week, combined with Estriol for the outer bits, starting with 14 days continuously and then tapering down the cream to every other night or twice a week while continuing with the Vagifem indefinitely.
You might also want to consider one of the laser procedures that treat VA by stimulating your own tissues to increase collagen production where it is needed. The Mona Lisa procedure is the most commonly done but the Intimilase or Renovalase lasers are pain-free and I believe available in the UK and very widely available in Italy, France and Spain. I thought they sounded crazy when I first heard of them but I have seen so many reports by women saying these are life-changing procedures that I think it is very worth looking into. Its 3 sesssions 6 weeks apart followed by a touch up once a year after that. Its not cheap, but then, this is misery.
The urologist will probably want to do a cystoscopy, they usually do, and thats not unreasonable when a patient presents with blood in the urine. I would suggest however that you give the HRT and the local estrogens a chance to work first and if you get better and the blood in the urine disappears, then you wont need to. Don't expect the urologist to know anything about estrogen and the urethra or the bladder, you would think they should, but they almost never do. Ditto most gynecologists.
Good luck