If the docs arrived with the SSN on everything, Id include the full amounts on the 1040, then make adjustments on Line 21 for the retirement that will go over to the 1041, report full amounts on the 1040 for the 1099B entries and and then make an adjusting entries on the Sch B and/or D for the amount being carried over to the 1041....that way you'll avoid the CP2000 cross matching issues.

If they arrived with the EIN on everything, then same idea, just opposite.