I had similar issues in my re-build
Summary is on
Post 243 in my
build thread
Make sure you're measuring as close to the wristpin as possible and are getting accurate repeatable measurements. Non repeating measurements threw me for a loop. I ended up with a similar difference in piston protrusion on my #1 cylinder as well - which is curious.
Generally speaking, you have plenty of room to play with given 0.035" piston protrusion.
The rough math is that each 0.001" of piston protrusion will change your compression ratio by ~0.1 point so as it sits cylinder 1 would be ~0.5 lower than the others. Not the end of the world, but obviously better if you can get rid of it.
There's a myriad of possible causes - block, crank, rods, bearings, pistons, dirt, etc.
I don't mean to keep beating a dead horse on the measurement method, but are you sure you're at TDC on each piston, individually, always approaching from the bottom and from the same direction of crank rotation, never going past (and if you do going back 45 degrees and making sure all the rings are pushed to the bottom of their grooves, etc). I spent an entire weekend figuring this stuff out the hard way.
Once you've confirmed that you have accurate and repeatable measurements on both sides of the piston, you can start swapping rods/pistons, flipping the rods 180, etc to get the most even protrusion across all the cylinders.
Be patient and careful, put something soft under the engine so if you drop a piston you don't damage it (speaking from experience here). You'll get the right combination.