200 executions of a query taking 6 seconds means that each execution takes 30ms to execute and return results, ignoring the parse and compile time (and SSMS is often slow to display results). Doesn't sound too odd.

If you're trying to identify performance problems, don't use fake setups like that, look at the actual queries that the app executes and test those, preferably. Unless the app really does run a particular query in a loop hundreds of times, testing and tuning that is not going to show you anything useful.

You say all the queries are much slower. Can you find a query that is significantly slower (run once, not in a loop), update the stats on all the tables that it references (you need to do that when upgrading a database from SQL 2000), then if it's still slow afterwards look at the wait stats and execution plan, see what the expensive operators are and what the query is waiting for.