It's kinda obvious you really want the 400 instead of the 440 block. Take the hit and get the kit for the 400. It is simple enough to build what you had and achieve what was needed. ALL STROKER ASSEMBLIES need more than just balancing. Something will not be perfect and have to be worked on. Wrist pin or 2 too tight, crankshaft journal needing to be a little flatter, rod side clearance needing adjusting...ieieie..
Your kit was probably around .012 or so in the hole for piston to deck height. You didn't say stock stealth heads or cnc ported. The chambers sizes need to be addressed. I usually do or have my engines balanced local. Once you have that 400 block assembled, let us know how it runs. Hughes doesn't make the kits, only supplies the parts and does some machine work. Even 440 sorce kits need machine work. You will be pleased with any direction you go in once it is machined, assembled and you hammer down.