I think maybe my machine shop either marked my rods wrong or put them in backwards. In these 2 attached pictures of 1&2, you can see that the rods are not very well centered on the wrist pins. Does this look right?

My pistons rods are clearly marked with a 1 and 2 stamp and my new pistons are installed dot pointing forward but these just don't look quite right.

 

If the rods have all been balanced the same then it doesn't matter which position they go back in. If they haven't been balanced then it still won't really matter where they go back.

If everything has been properly balanced then the rods should all be the same and the pistons with wrist pins should all be the same. As long as the rods are installed properly on the crank, it doesn't really matter which hole they go into. If the block was machined properly, each hole should be matched with a specific piston.

 

Correct piston/rod orientation puts all 8 bearing tangs facing "out", away from the cam; as well as of course, all 8 pistons facing the right way.

The pin is designed to be quite a bit shorter than the pin bore, and the piston leaves lots of room for the rod small end. The rods are located positively along the crank, ± a few .001"s, and of course the pistons are located by the block. Blocks are RARELY machined very precisely; the tolerances in the block (cyl location front-to-rear) and in the crank, mean that the rods are almost NEVER centered in the pistons.

If the rods are backwards, such that the bearing tangs are on the side facing the cam, the bearings usually won't fit; they're not symmetrical, they're wider toward one side than the other, and if they're backwards, the wide side (which belongs facing the adjacent rod) will instead be riding on the radius where the rod journal meets the throw, and the motor probably won't even turn.

Rod side clearance, i.e. end play along the crank, should be around .010" or so; no more than .020" for sure, preferably less than .015", but at least .005". You should be able to slide all 8 rods from front to rear on the journals with minimal effort. The pin should of course slide front-to-rear in the piston at the same time. If the rods are all free to move that little bit, then it's most likely all OK.

Your pictures are too blurry to tell what's going on in your case.