I would leave the engine and tranmsission stock for the time being. I'm not sure that I would gut the car either.
Here's what I would do, if I were in your shoes. I would find a decent 1989 Civic Si or CRX Si and leave it alone. Then, I would go through the car and replace anything that is worn out or broken. I would flush the brake fluid and replace with Motul 600 or an equivalent. Replace the brake pads with a good street/autocross compound, something like the Carbotech AX6.
Once that stuff is done,
I'd start learning how to really drive. Leave the wheel size stock, and get some stickier tires and go stock class autocrossing and start doing HPDEs. HPDE is high performance driving education or track days. By stickier tires, I mean something along the lines of Falken Azenis RT-615s or
Bridgestone Potenza RE-01 (I think thats the new Bridgestone).
Once you have a little experience, then you can start with the chassis, brakes, and
suspension upgrades. At that point, you'll have a better understanding, hopefully, of the autocross rule book, as well as, knowledge of how the car will handle on track. Then you can start throwing the really good go-fast bits at the car.
My car is a couple of oe parts short of being a Si. The only mods worth really mentioning are the e-bay header and 15" wheels and tires. Suspension is bone stock, except for the Mugen rear trailing arm bushings.
The last time we all went to the mountains Jeff, or JFRO, had a hard time keeping up with me. He was in his boosted b swapped CRX, there's a thread in here about the car.
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The best car you will ever make is the driver mod**