so if I purchase this new property as Joint tenants with a Declaration of trust 99% to 1% in favour of my wife
Tenants in Common. It's not possible to have a 99%/1% share as joint tenants.
Question 1 - what is the impact of this if we chose to mortgage the property in due course?
It should make zero difference. This is an absolutely bog standard tenants in common ownership. You do not even need to have a express (written) DoT in place, just that it makes it easier for HMRC purposes to prove the ownership proportions. The only thing mortgage companies care about is that the legal and beneficial owners are the same people. Some will refuse to lend if they are not.
Question 2 - if we change the proportion at a later date, is there any impact with HMRC (at present), or is it just 'OK'?
Assuming you're married then there's no CGT impact. But if there's a mortgage then the liability is deemed shared in proportions equal to the actual ownership. So a transfer of ownership might incur SDLT. (Note that some accountants say you can decouple the liability from the ownership, others say you cannot, and I have no idea which is correct - or even which is the majority view)
See example 3 here: https://www.gov.uk/hmrc-internal-manuals/stamp-duty-land-tax-manual/sdltm00330a
Also https://www.legislation.gov.uk/ukpga/2003/14/schedule/4 paragraph 8 section 1B
The legal question is whether you can use 8(1)(b). I don't know whether 8(1B) defines the 8(1)(b) transfer quantum or explicitly excluding a transfer of liability in a DoT causes 8(1)(b) to trump 8(1B)
Question 3 - can we do this retrospectively to the other properties we own jointly?
Not retrospectively - you cannot "backdate" a transaction but you can change the proportion of ownership going forwards.
But see the comments to Q2 regarding SDLT. (You can also put a property currently in sole names into joint names - by putting it into joint names but keeping the ownership 99% to the original owner, 1% to the new owner, you can split the income 50/50 for tax purposes but avoid SDLT as the new owner will have a negligible amount of deemed liability on the mortgage - you would not submit a form 17 in this case)