I'm assuming you already have a factory assembled OEM ej257 shortblock? If so then I would call it assembling a long block rather than building an engine per say.
First thing you're going to want to do is fully disassemble the heads thoroughly clean and hot tank everything. Then I would inspect them for damage/wear. Look for scoring on the cams/journals, valve->valve guide clearances, inspect the valves for pitting or any other visible damage (same goes for the head chambers). I would also check the spark plug holes for cracking. Replace anything as needed. Then I would chamber match the heads to the volume and profile of the B25/V25 head castings. A CNC lathe will be the best/easiest way to go about doing this. If you have the time it would be nice to deshroud the intake valves and give intake and exhaust ports a nice bowl blend.. focus more of your attention on the dog leg (#4) exhaust port since it's the one that flows the least from the factory (deshrouding and bowl blend isn't necessary, but if you're doing it all yourself it will be worthwhile to do while you have it all apart since it will be a free upgrade). You should check the mating surface of the castings to make sure they are true. If there's even the slightest warping then you need to deck them.. they will need to be resurfaced as well. Personally I would work the valves over.. if you have access to a radius cutter (ie. Serdi 60), then I would do a radius valve job. If not then 5 or even 3 angle will work. Then it will be time to lap the valves into the heads.. you need to ensure they are fully sealed when seated. Once you get the heads mostly reassembled you're going to want to set the lash (unfortunately I don't know the specific clearances to shoot for off the top of my head, but I'm sure it can be found online). You're probably going to need new buckets to get everything properly adjusted.
Once the heads are all fixed up and assembled the hard part is over. Use OEM ej257 MLS head gaskets, I recommend ARP 2000 series head studs (depending on your ultimate goals with the engine.. if you want to run higher than average boost then you will be better off springing for the Custom Aged 625+ head studs). Use the ARP lube and torque to ARPs recommended specs. There is a specific torque sequence to follow, but once again, I don't remember the specifics off the top of my head, but all this info can be found on the internet.
Then you have an assembled long block.. there's more to come after that, but getting it all together correctly should be your first goal.
