15 years ago or so, I installed a big bore kit and dual carb cam from AA to my 1.8L 75 engine. I ran the engine for 5-10 mins then did a emergency shut down due to a massive oil leak. The leak was due from me installing the push rod tubes and heads as one complete assembly. A few days after the first engine start up, a massive tree fell down in my back yard, and smashed my nine one four, and part of my garage!
Last year I acquired a tub and have been putting the car back together. I have decided to ditch the carbs, and go back to the original Ljet system. In order to do this, I had to re-split the 1.8L case and replace the cam to web-cams stock cam. I have watched Jake Raby's video numerous times, and noticed a ton of mistakes that I have done 15 years ago. The biggest problem I'm having right now, is removing the wrist pin on the number 3 piston. All the other wrist pins slid right out with no issues. I ended up using a swivel adapter and some extensions to remove the rod cap, and removing the piston with the rod, before splitting the case. I tried using a C clamp to help persuade the wrist pin out, but was starting to damage the piston itself. I will take the number 3 piston/rod to a machine shop and let them have a go with it. Or am I better off leaving the wrist pin in, and just spinng the rod and piston 180 out, so the arrow faces the flywheel?
The problem I'm having, when I assembled this engine, I wasn't mindful of the arrows for the pistions. Number 3 and 4 arrows were pointed toward each other, and I believe 1 and 2 arrows were facing the flywheel. Now, looking at the engine case, there are marks of collision where the piston his the case.

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number 3 cylinder

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number 1 cylinder

No marks are seen on the case for number 2 or 4 cylinders. Did this happen due to the arrows not facing the correct way?
There were gaskets installed, one on the bottom of each cylinder and one on top.
Also, can I reuse my solid lifters that I bought from AA? There is barely any run time on them, and I believe they are webcam lifters.

Hard to tell what caused those marks but I bet is not from mounting the pistons upside down.
The reason for the arrow is that some pistons have asymmetric pin position but that is just very slightly. Most pistons I've seen today, including AA, are symmetric but still have the arrow so there would be no questions asked.
Are you sure that mark was not there before the previous assembly?
Can you see matching marks on the piston?
I understand that the engine ran so it moves freely. Can you check if the piston slides out of the cylinder at the bottom end during engine rotation? You can just measure the cylinder length - stroke - piston height - deck height (1-2mm ). I bet you'll have some space left to prove the piston didn't hit there.

The engine did rotate with super ease, exactly like how Jake demonstrated in his video. I never saw any obvious marks on the corresponding underside pistons.

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piston1

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piston3

I'm at a loss to why I have these odd marks, and for now I'll turn a blind eye to them.
Towards the number 3 wrist pin, should I take it to the machine shop, or should I just reinstall and let sleeping dogs sleep? The connecting rod moves very nice on the wrist pin.

If I understand you correctly, you are having a hard time moving the wrist pin from the piston? Heat it up a bit and it should slide right out.

The wrist pin is probably blocked by a deformed pin hole, after the c-clip holding it in place. I think that you'll kill the piston trying to take the pin out. Maybe you can try to drive it to the other side.
If it doesn't go out nicely and you can re-install it as is, I would just put it back on a different cylinder to mach the arrow direction. BTW, you'll see that Jake video says that the con-rods should all be with the serial number up but that's BS as they are completely symmetrical so no worries about that in positioning the piston.

Are those AA pistons? I have a similar 96mm set and some claimed those are NPR

At this point, I can't be certain what I bought from automobile atlanta 15 years ago. I want to say yes, that they are AA pistons, but I'm not sure. Here's a crappy pic of a manufacture logo stamp on the inside of the piston.

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Yes, I have some marking on mine as well. The markings on mine look blurred without the out-of-focus picture so I can't find what make they are.