First, you should understand that instance-store is not necessarily faster than EBS for all use cases. It depends on your read / write patterns and can get complex to predict. Fortunately, EC2 lets you run different configurations for short periods of time for very little expense, so you can try out different ideas and see which one gives you the best performance.
There is a huge first use penalty for EBS block IO and a first write penalty for instance-store block IO, so it is important to warm up the disks before testing performance.
EBS IO can sometimes be improved by running an instance type with larger IO bandwidth. For example, if you are running an m2.xlarge, you might try upgrading to an m1.xlarge.
All that said, if you still want to switch to instance-store, you cannot convert an EBS boot instance directly to an instance-store instance. You will probably need to start a fresh instance-store instance, install and configure your software on it, and copy the data over to the local ephemeral drive(s).
On Linux, there are ways to create an instance-store AMI directly from the disk image on the EBS boot instance, but I'm thinking that may be tougher or impossible on EC2 Windows.
As with all instances, EBS and instance-store, you should plan for and test instance and disk failure, making sure that your valuable data is secure in other places.