Well I don't like to disagree with medics generally, but if she's still taking a good feed at night and it doesn't seem to be affecting daytime feeding then I'd personally keep it for now.
It sounds like she's still doing well on self setting in general, that's great
As for ideas on how to wean coming into bed with you when you're both ready... Well, there's still the hand in cot thing if you lower the mattress, right? Or is that not possible with her cot? I seem to remember reading somewhere about Tracy actually climbing into a cot to lie with a baby (!) who was having trouble weaning from co sleeping - but I really doubt that would be necessary since she settles well otherwise. I'm kind of hoping that once she's feeling better and the routine settles down (transitions tend to be quite bumpy, so this may be all it is, once she's settled on her two naps you may get some stability for a while - let's hope so anyway!), then it should be easier to get her back into independent sleep habits at night. It may be that she protested for such a long time previously, because she was in discomfort or UT/OT. Is she especially spirited? Spirited LOs (and their parents!) often have a harder time with this sort of thing, especially if they're very persistent, so I think whatever you decide to do, consistency is key. There are lots of other parents here with spirited LOs who I'm sure have lots of tips, and of course hands to hold
As for your other question re timings of NWs - I'd pretty much say the same as you, that the early evening wakings are more likely to be OT, but bear in mind that OT wakings can be a little later too - I was convinced our DD must have been UT when she started 1-2h regular NWs around 11-1am, so kept pushing BT until one day she was so tired we went for EBT and discovered that that was actually her preferred BT - so we kept it there! The other wakings that could be OT is when they 'crash' at BT but then do a short night, typically less than 10.5h. Sometimes if the night is very short they'll get back to sleep again eventually, so a waking around 4-5am (with or without resettling) could still be an indicator of OT. But yes, UT wakings tend to be characterised by cot parties, or else EWs where LO is happy and remains happy throughout the morning, not showing more tired signs than usual. This is just from my experience and those of others I've known - of course every LO is an individual and you will know yours best
Sorry to ask again - would you like your GS thread locked, so you can have everything in one place here? If so, would you like us to bring your GS post over here to merge with this thread, or just leave it?