I agree with your approach here OP. Given the obvious evidence that this engine was used hard, it doesn't make sense to do more than the bare minimum to fix the observed issues (piston, small end bushing) and put it back together. No reason to go nuts with fresh rings and bearings everywhere but not take the block out for a rebore and fresh pistons and intermediate shaft bearings. I think the only reasonable paths would be a minimal route like you're doing or going all in on an overhaul. Anything in between is diminishing returns.
And yet, you may get quite a bit of life out of it with the quick and dirty approach. I did this same move once with a 1Z that swelled and partially melted the middle two pistons after the PO towed his boat up the local mountain pass on a 110F day foot to the floor with a pair of hot Upsolute chips in the ECU (not sure what some folks expect when they attempt this? I see diesel pickups on the side of the road on the high passes every summer day with hoods up having done something similar LOL). Anyway it had scored the bores pretty bad, worse than yours, and only was running on about 2 and a half cyls. When I got it I didn't feel like putting big effort or money into the motor until I could drive the car and see if it'd be worth it, so I just popped those two pistons out, ran a hone until the vertical scoring was at least not as easy to see, grabbed a couple of lightly mashed pistons I had from an ALH that had snapped the TB years earlier, and dropped them in. Reused their rings and the bearings, and didn't even touch #1 or #4. I think the only new parts that went into that job were a headgasket and pan gasket.
I didn't expect much from that frankenstein hackjob motor, but it fired right off and ran clean immediately, never used a drop of oil, and had no issues whatsoever for the rest of the time I had it till transmission issues took the vehicle down. I'm sure it probably would not have given another 300k, but it would have probably put on 100k without breaking a sweat.