Best bet is to simply import the data from your converted FMP 5 files into new files. In Import records, you've got a new table option that'll enable you to both import the data and the field definitions in one step if you care to use that method. (You may have to edit some calculation fields after import.)
You'll also be able to selectively import converted scripts and/or copy and paste layout elements from your converted files if you so choose.
Final recomendation: If you don't have FMP advanced, scrape up the extra dollars and get it. The database design report and script debugger will be invaluable to you during this process.