The 390 has a bore size of 4.05, the 406 is 4.13 (same as a 428). A 390 would have to be bored .080 to be a 406 leaving the cylinder walls pretty thin unless a 391 truck block was used. The majority of 390's have hydraulic lifters, the 406 has solid lifters. There were some 390 high performance and police engines with cross bolts, very rare, and not all 406's had cross bolts. The basic answer to your question is yes.

Sources: ford muscle parts, holman moody

the casting numbers for the390 are different than a 406 in the HOLLANDER INTERCHANGE MANUAL.My memory is trying to say that the 406 had cross bolts in the main caps to strenghen the lower end.had a friend that had the 6 pack engine blow a flywheel on one .he also lost hood,firewall and windshield .cant go from 2nd to3rd at 100 mph.