When I say rationalise the data I mean make it so its usable/relational (At the moment if I use bulk insert I can only insert into one table)...
It would be ok if Sql Server was fast enough at text comparison but no matter what indexes I place on the tables I am unable to get the data out fast enough.
Also on your MSDE comment, MSDE is restricted as to the amount of data/connections you can have at one time.