Why does this happen and what to do?

Got this 6.1 sitting (heated garage) for five years or so and finally got to it. Only 27,500 miles (that's what I was told anyway) but had a rod knocking sound after half a minute after start. Found a spun bearing so went shopping and found a crank and rods from a new engine. He was building a stroker on a new engine. Also bought new crank and rod bearings.
Why does it happen and is there a cure?

Cyl and crank on 1,2,7 and 8 looks good, but 3-6 are not so nice.
You can barely feel a couple of scratches in 3 and 4 cylinders.
A honing job should be enough I guess.

Will I have to replace the pistons or would new rings be enough?
I'll try to post some pics.

My plan is to drop it in my 71 Sport Fury and run an A518 behind with 3.91 gearing and 28-29" tires.
Have been looking at a MegaSquirt box to control it. Have a friend who works at a company with a chassis dyno and he's used to working with MegaSquirt.
The car will be driven a lot, but I'm not gonna be too hard on the revs.

Off the top of my head, I would be measuring everything, especially the bore.

-Might not be round
-Might not be cylindrical
-Might be too much clearance piston to wall
-Probably not because the skirt is real short and the pin real high allows it to shingle
-And even if the bore was good and round, over heat it, and it won't be after that....
-Piston squirters plugged?

The skirt and cylinder wall is from bearing material embedded in the skirt. It probably had 27,000 on it when someone hurt the bearing in it. The pistons are junk now.

Heat

So that means I will have to replace at least some of the pistons, probably all...
It also means that I need to have the bores checked for roundness.

Could the cam be hurt from debris as well?
I read somewhere that some of the engine bolts not can be re-used?
And valve springs should be replaced?

At this point it feels like a stroker kit could be an option...
What would You do?

Ditch the stock junk. Put good stuff in it.

Swapping pistons and rods from other motors are what 5.7s are for

Don't have a 5.7, mine is a 6.1.
Anyway, I can either get new pistons or try to sell crank and rods and get a stroker kit.
Is there any other upgrades you recommend such as oil pump, valve train etc?

I have boxes of good pistons and rods from 6.1's that have been turned into strokers. For sale cheap if you want em. OE oil pump is just fine. I like cubic inches so I always stroke em but what are you planning to do with it and how much power are you after?

I just want it the way they come. I would love to build a stroker but I'm on a budget. With no cats, open air intake and some tuning I hope it will be enough in my crusier. Guess it will give some more hp over stock, and with the A518 it wont loose as much as with the original auto tranny.

I'm wondering what I can reuse, the scuffing in the coating is worrying but I might be able to remove the coating, do some home honing and put new rings on?
I'll give it try and if it not turns out the way I hope, I'm interested in your pistons for sure.

People are talking about bad valve springs as well. Aren't they good enough for my needs? I haven't heard of any failure in any of the forums I've read.

The engine will barely see rpm's beyond 5,000. I will use it as a daily driver.
If there's any trick to move the power and torque peak down I'm interested to learn. I'm willing to loose top end to achieve that. Advance the cam?

Where do I find bolts and gaskets? I'm not gonna pay hundreds for ARP bolts just because...