Dream on.

Well I ain't no scotty, and I agree with @Doc - that'd be the ultimate suggestion. 😆 

but anyway here's some answers as I see it:

Toyota Camry or Honda Civic?

These are not two things that'd you compare. two different sized cars... kinda like comparing a Yaris and a Corolla - or a Fit and a Civic, you pick based on what you can afford, condition and size.

As far as new cars? Civic vs. Camry? The Camry is a foot longer, a bit wider, the 2.5L 4 cylinder and the V6 come with a conversional automatic gearbox and not some trashy small cvt - it's on a whole different level.

I've seen videos that Skotty says Toyota engines are good and they have asin transmissions and asin transmissions are the best transmissions out there.

A lot of companies make great engines - Mazda's SkyActive is great, Ford's DuraTec HE is great (powered the previous gen. Miata), even VW had some gems like the GTI 35's EA113. There are plenty of good engines and transmissions.

Aisin? well they have some good products, some awful products - I wouldn't go praise them. Some of their transmissions like the K1XX are garbage, some like the U660E have had terrible premature failures - some like the AW55-50SN ruined an entire car brand! but most models are alright.

It's not like "If it's aisin it's good" - some Asians installed on Camrys have defective torque converts and fail at 70k miles (you can find many instances of that on this forum)

But on some videos he says that honda makes the best engine. But I don't know what transmission honda uses.

EarthDreams has stripped Honda of that title. Honda transmissions are usually of their own design or Yamaha, sometimes Aisin.

Is there a way to marry a honda motor to a asin transmission?

cars are not lego. some came with Aisin transmissions as far as I know the 2018 Ridgeline had an Aisin but it's just not good at all generally.

In a nutshell my main question is Toyota Camry or Honda civic?

Mid-size vs. Compact - depends on years, needs, pricing, ... but generally Camry.

When I purchase either vehicle I want it to at least have 40,000 miles on it but no more than 60,000. So it has somewhat been broken in and has hopefully found out all the problems.

First you need to earn that kind of money - and no, on a Toyota? what kind of problems bellow 40k miles are we talking about? usually there's none.

Ps. If there is a Lexus or a Acura that has the same motor and transmission as the Camry or Civic please include that as well.

Acura comes with ZF 9HP are it's worthless junk.

"Same engine and transmission" the Camry is offered with at least 4 transmission and probably 10 engines. what powertrain exactly? 

Anyway the Civic shares it's platform with the Acura Integra, and Camry shares it's with the Lexus NX and ES (much better cars.)

It really depends on what you are looking for. Slightly bigger: go Accord/Camry. Not too big not too small: go Corolla/Civic. 

I personally like Honda’s interiors better than Toyota, but that is personal preference. 

As an overall car inside and out, I like the naturally aspirated Civic. The civic has come a long way. 

If you asked me this question 20+ years ago, I’d be all about the Accord. 

You are talking about two completely different cars as far as one being a big sedan and the other is smaller sedan so deciding between the two depends on your needs from the car you are purchasing. But even though the Civic is known as a smaller sedan compared to the Camry, they're still pretty big compared to like those from 15 years ago. Japanese cars have all become bigger over time.

There's no need to buy one with at least 40k miles to make sure they've found all the problems. You're talking about Toyota and Honda and cars they've been making for so long so I don't see anything wrong with purchasing even a brand new one. This part of your question reminds me of my home country that people pay more for used cars and actually prefer used ones because the initial owner has fixed the problems the car came with. But this is because they don't have good quality cars; they have garbage cars basically. One example is they had put air conditioner hoses instead of hoses specific to gasoline so any person who had bought those cars new had to get this fixed. But with Honda and Toyota you're not going to see these kinds of problems. I've bought new Honda and Toyota cars multiple times and never had issues with them.

Below is a video from Scotty about the new Honda Civic; even though they have cvt and some are turbocharged I wouldn't worry too much about it. If you are willing to spend more and can drive manual the Civic Si or even type r are nice/good cars, but definitely test drive them to see how you like the ride.

https://www.youtube.com/watch?v=KN1ILMpzsk0