Hi Antsu,
This is a great question. The data import tool will work but will be a bit time consuming. Do you know how many rows of history data there are for each point; can you export the entire history and view it as csv in excel?
Another option would be to export just the pointValues table from the mysql database and import that into the new MA mysql database, the problem is that dataPointid reference may not match up by default so you would need to go through and make sure they match. I've played around with this awhile ago and it can be a bit difficult to get right.
Look at the dataPoint table in your old version and the the new version and make sure the id matches. I believe that Mango created the data point ID based on the order it is imported so you can rearrange your data points in your import text so that the point ID's are created the same as in your old version.
This is all very theoretical so would like to hear back if any of it works for you.
Joel.