I do product development and I've never been able to do a project based on engineering at home or honestly at work. The 1 course that helps the most is the one I kind of took by mistake, anthropology. Its helps me with the VOC (voice of customer) stuff and VOC is how everything begins.
Henry Ford didn't feel that way and once said "If I asked my customers what they wanted they would have said a after horse" or similar. He took that to mean there was no point in asking, but what I tell my teams is that people explain in terms they understand so you usually need follow-on questions like:
how far do you need to go usually?
how many people come with you?
do you need carry stuff too?
and suddenly the faster horse they are describing is a car, they just didn't know that because they'd never seen one.
I says all this because I hear technical terms and solutions before I'm hearing what exactly it is you want to build. Please forgive me if you know all this but it was sounding like the project is a bit adrift and basic goals are how I like to stake projects down.
Step 1 is what do you want?
You want:
A 246GT with modern performance. Yes?
Mostly stock looking exterior because its pretty darn good looking as is. yes?
Interior of donor is missing and stupid expensive to replace so this will be modern street/race finish. Yes?
Street "legal" as in registered to drive on the street. Yes?
now it gets harder.
Street legal can mean a lot of things.
My 308 has illegal brakes and excessive noise so by legal I mean it can be operated with low chance of being cited for the violations (which would ruin my day).
I want to be able to get in and out so a proper roll cage is not an option.
I want it to look factory to the untrained eye...ferrari guy will spot the mods a mile away but ford guys won't.
I want to be able to drive to local autocross events, so tolerate the ride and noise for up to 90 minutes.
I want to drive on local roads....so that limits how low and how stiff the suspension can be.
I want to be able to let others drive it...so I need to watch how hard the brake pads/pedal are and how stiff/digital the clutch is, maybe valet mode and traction control
It needs to pass (or mostly pass) state inspection so all oem lights, wipers and such.
Just 1 simple basic thing turns into 1/2 dozen specs, that for me are worth writing down, because now I have a plan I can follow, when I see a part on ebay I can buy it knowing I'll use it.
...but there really was no engineering in any of that and I'm about to argue the same is true for most of the rest of the design rough out.
Engine choice
Engine says and Honda would do, set the required output then select the lightest option to achieve it that says in budget....and the answer is always a 4 cylinder as that will get you 1000hp with a turbo on even a modest budget.
so the real questions are
What do you want it to sound like?
How much vibration do you like to feel? Flat crank V8s shake a bit so the effort goes into smoothing it, Vs a straight 6 or 12cyl that are silky smooth so often you want to transfer some of the shake on purpose.
What do you like to look at in the engine bay? You said ITBs I thing so why? to look at? meaning covering them with turbo stuff is bad?
I would argue this is a pretty import place to spend time....drive a few things maybe, look at a lot of pictures. Its way more about what you like than engineering.....Ferrari builds V12s because Ferrari builds V12s, the engineering reasons died in the 1960s or 70s when valve springs got better. BMW does straight 6s because they are smooth, but so are balance shaft 4 cylinders. I think the 12 or V8 boils down to how stuffed do you want the engine bay to look?
Then hp. how much? Hooking up more than about 400-450 is a challenge and like a 308, the 246 is very short wheel base so unstable at high speed meaning that even once you get it moving lot of hp isn't really helpful. The hp number tell you the size engine you need or if you'll be running boost. NA vs boost sound completely different and I would argue this is about the biggest consideration to how the car makes you feel driving it so I would say make that call early and work backwards from that choice to pick/design the engine.
Once you pick the engine.....well it needs a transmission and that will kind of determine what direction the engine gets mounted. At 92" wheelbase the car is going to turn very well and I seriously doubt you'd ever be able to actually measure a different the resulted from the engine orientation or a couple inches of engine CG change, but if you thing you will be able to measure it then you need a turbo honda 4cyl because all the engineering says that is the right choice
That's how I do this stuff, so hope it helps, if not then by all means ignore it.