You changed from 32 bit to 64 bit and changed from SQL 2005 to SQL 2008 at the same time. I also assume the hardware changed - is the old hardware still running?

After upgrading, did you rebuild all of the indexes? This is important during a SQL version change.

The first step for performance tuning is to look at the execution plans. That is why having the old hardware and database would be nice, you would be able to compare the execution plans pre-upgrade to those after the upgrade. Since your process sounds like it is running a lot of small queries that are probably very similar, a few minor changes can have a big impact. Focus on the individual queries and their execution plans, any of the changes you have made could impact the plan generated by the database engine.