I agree with the others that systemic HRT may be a very good idea. Months since I looked at the forum so I am out of touch with what's been said recently, but if you have a menopause clinic nearby they are often a better source of advice than GP surgeries unless you are lucky enough to have one with a really knowledgeable GP interested in Menopause. But I'm guessing they might not refer you there unless your bloods show you are menopausal.
Vagifem just twice a week may not be enough, with or without systemic HRT. As already mentioned, I would ask for Estriol 0.01% cream (the weaker preparation) to use externally in addition to the Vagifem & perhaps ask whether you can increase the number of Vagifem you use per week. Even after 2 years on systemic HRT, 2 a week were not enough for me. It was suggested I use up to 5 per week - equivalent to the former 2 x 25mcg strength, together with the weaker Estriol cream applied thinly externally. It took several months after increasing to 5 a week with Estriol on the same nights, before I really started to feel comfortable & robust.
If it's approved for you to increase the number of Vagifem & you are happy with this, the advice I had from the Menopause Clinic was to either double up to keep the total number of nights' use to a minimum - i.e. inserting 2 a night - 1 high, 1 low, or carry on with just one a night if you prefer (either way up to a total of 5 per week if approved), but try varying the positioning. Vagifem can have quite a localised effect, so inserting one lower down helps ensure more of the canal is effectively treated.
The Estriol cream is very soothing - I can feel a difference in comfort immediately after applying, but both Vagifem & Estriol take time to return the whole area to good condition & it may need up to 3 months at a higher dose, so don't give up hope.
Also, after showering & gentle towel drying, maybe try gently pressing soft tissues onto the external area to soak up any residual dampness, that can otherwise lead to soreness & cracking when the skin is so delicate.
Just a thought - you said they checked & there's no obvious reason for the spotting - if you kept your cervix, is your smear up to date?
I hope you get some good, sympathetic advice from a Meno Clinic or knowledgeable GP & soon start to feel much better. Good luck with it.