I think some posters here are being unnecessarily harsh with you.
You took the morning-after pill within twelve hours of your one-night stand and had a subsequent sexual health check-up. Yes, you had unprotected sex, but you took action quickly and responsibly.
You got back together with your ex and decided to stop using contraception and start trying for a baby immediately. Though there are lots of posters here with something to say about that, it's no one's business but yours – and it's not what you came on here to ask about.
It sounds like you've also communicated well with your partner about the situation and you've been honest about your one-night stand, even though you were single when it happened.
The length of a pregnancy is measured from the first day of your last period, with the due date calculated by adding 40 weeks. The number of weeks that have passed since the first day of your last period is the gestational age.
Fertilisation age (also known as embryonic age or fetal age) is the number of weeks since conception. Though every woman is different, on average this occurs around two weeks after the first day of your last period, when you ovulate. So when we talk of pregnancy lasting 40 weeks, we mean 40 weeks gestational age and 38 weeks fertilisation age. (Those extra two weeks in gestational age are pre-conception.)
On 16 July, the doctor estimated gestational age at 6 weeks and 1 day, which means first day of your last period on 3 June and estimated conception on 17 June.
I'm not sure if this was at a different appointment, but you were also given an estimated due date of 4–7 March. This gives you an estimated date of conception of 12–15 June (with estimated first day of your last period between 29 May and 1 June).
Based on these dates, you conceived this pregnancy in mid June with your boyfriend –not the one-night stand.
For further reassurance, you took the morning-after pill within 12 hours of your one-night stand, so it's very unlikely that you'd be pregnant from that. It also sounds like it brought on your period early, on 1 June (which fits with estimated gestational age). The pregnancy tests you took in the first half of June also came back negative.
You're second-guessing yourself because you're anxious, which is totally understandable. You came on here for information and advice, and it's a shame you've had hurtful comments thrown your way. It's a curious approach from some people – writing judgemental comments and telling you to educate yourself but not bothering to answer any of the questions you raised in your post...
Best of luck to you, your partner and the new baby xx