I tested out doing it in separate entries and it still errored on the Sch D total gross proceeds, can you override that field? or will it just not take that many digits?

Im honestly not sure what the workaround for this is. 

You may need to prepare a Sch D and 8949 manually (you could attach to the return, but the chances of a human seeing it are slim), make sure your net gain/loss on the return is correct and be ready to send your manually computed forms and explanation letter in response to the CP2000 letter in a year or two when they tell you your gross proceeds dont match their records.