pony conecting rod question ?

Pistons in the same cylinder is not critical because you honed the cylinder and installed new rings.
This means the piston/cylinder marriage was broken, now on breakin they will remarry.
Rods? That is a gray area... Rods with new bearings installed, mixing and matching caps numbers may not be so critical but orientation could vary well be an issue as in some rod designs the beef of the material may require a specific orientation.

Jessie, my opinion is that those considerations are less important than making sure that the bearing clearances are within spec, the rod and rod cap are matched, and that the rods haven't previously been stressed. All the other stuff that goes with it is important too: clean, undiluted oil, good crank bearing clearances and all bearings firmly in place in their housings. Those ponies have a habit of the main bearings working loose and then you get lots of end play that can result in broken mag gears and possibly broken rods

so just to play it safe im guessing I should pull them back out rotate them 180 and not take any chances...Why couldn't I have accidently put them in the right way , it never seems to work out that way ...thanks for the impute

Although the bearings should be locked in the connecting rod by the "crush" of a properly sized big end, the locking tabs should be oriented the right way so the edge of the little tab on the bearing insert half bears against the flat surface of the opposing connecting rod or cap, positively stopping any tendency of the insert to rotate in the rod. I have heard that the tabs are more for locating the insert axially in the big end of the connecting rod than to prevent rotation.

The larger pony motor on the D318 shows 4 oil holes on the rod which I believe could be oriented either way and still provide normal lubrication.

So, even though I suspect the engine will run just fine with the rods installed upside down, I think it would be better to turn them over.

That would be a true statement when it was New!
OR had easily obtainable new parts at realistic prices.......
By the time you get that Antique, chances are you will be surprised what some farmer/shade tree mechanic has inside of there!
I remember taking a perfectly running babbitt bearing engine apart and finding all kinds of combinations on the rod bearings. Every journal was perfect condition!
Read lots of the OLD books for various farm tractors and you will see that in SOME CASES, IT IS ACCEPTABLE to put back in what you found!
If matched pair rods for a D2 pony are not obtainable brand new, then put back in what you found, how you found.
Thats all I'm saying!

If there were 3 dots on one rod AND cap and 4 dots on the other rod AND cap, the 3s should stay with the 3s, with the dots both top or both bottom.

Generally best to leave things as they were--I've come across an Allis Chalmers engine that had the rods offset fore and aft on the crankshaft. Didn't want to go together with one rod rotated from the original position.

I think you're on your own as far as "official" torque specs on the ponies, but here is a generic fastener torque chart for guidance.