So which one of these questions would I answer? Because for 5a, I have not technically been refused entry at the airport, etc.....would I answer 5b?
Yes. You answer the one that applies to you. If they both applied (i.e. you had both been refused entry at the border AND refused a visa by applying in advance) you would answer both.
As I've said, I do not have the refusal paperwork (it was 3 years ago and my guess is that I was angry/did not think I'd need it again!), but I do have an estimate of the time. Is it worth including my Tier-4 acceptance letter too?
Not necessary... you just give the details of the refusal (as best you can), i.e. visa applied for, when you applied/when it was refused, reason for refusal
If you have any reference numbers or anything like that, you can include them. If not, they'll just have to look them up for themselves.
For the cover letter to explain the refusal, can I say something like:
I applied for the Tier-4 (General) Student visa in July 2015.
I was refused this visa in August 2015. I misunderstood and did not submit the required financial documents.
Unfortunately, I do not have the official refusal letter.
However, I applied again and was issued a visa September 2015.
Yes, something like that would be fine, although you could include a little more detail, such as, 'I applied for a Tier 4 General student visa in July 2015, to study for X degree at Y university'.
You will have been issued with a refusal letter originally, so it might be better to say 'I no longer have' it, rather than 'I do not have' it (which implies you didn't get one at all)
[For future reference, always keep all your paperwork from anything like this - as you will also have to list your refused visa and the details of it on future visa applications]