The challenge is mapping data elements and logic between the two systems. And you will need to do custom coding for that. Probably a LOT of custom coding.
My advice would be to load the legacy data into staging table in your new database, and then draft sql procedures or scripts to transform it to your new schema. This way the process is repeatable if logical errors occur.
And my advice would be to get a competent DBA to help you with this and expect it to take a couple weeks to get it right.
If it's not practically useful, then it's practically useless.
Basically, what was needed then was to migrate all data from a proprietory db to MSSQL. Luckily, we were able to connect to that database through ODBC. We added that to MSSQL and from there wrote scripts to do the migration.
I agree with blindman, you may need a lot of coding to do this. We spent few weeks to do it cause almost everything (table structures, fields, etc) is different.
It's not difficult but you may need time to do it.