He said to swap out Pistons 1 and 4 since the #4 piston cylinder typically runs the hottest. Is it ok to move pistons around?

I'd guess it won't cause low compression or oil usage, that depends mostly on how you set your ring gaps and how you CC the head/piston dish. Might cause a tiny loss of power or increased wear over the next 100,000 miles. More piston slap? Datsun tolerances are already higher than Detroit of the same era, so it probably won't hurt

Maybe you can swap pistons around until they are all in spec

So the machine shop measured everything and still got it out-of-spec -- which happens all too often. That's why I prefer to do it myself

Motor was honed out and stock pistons were measured by machine shop and read as follows:

Piston 1 2.9922
Piston 2. 2.9926
Piston 3. 2.9924
Piston 4. 2.9929

All the bores read between 2.9940-2.9941

Clearance is

1. 0.0018
2. 0.0014
3. 0.0016
4. 0.0011

Nissan specs are 0.0009-0.0017. Engine is being built back to stock standards combined with a mild cam regrind from Isky, GX head and dual Hitachi's. Do I need to be concerned about #1 piston bore being out of tolerance that could lead to oil consumption or low compression?