Need to run a business rule before checking the transformation rule.

To capture the moment just before transformation rules are processed, this would be a rule type of TransformationEventHandler, so you would have to put your Extender Rule code into a TransformationEventHandler, where you filter on this particular condition:

If      args.IsBeforeEvent _
AndAlso args.OperationName = BREventOperationType.Transformation.ParseAndTrans.ProcessTransformationRules Then
 ' -- do your stuff just before transformation rules are processed --
End If

However there are two items to be careful about:
- I would be very wary about dynamically updating Transformation rules on the fly (as the question suggests) from a BR that is triggered just before the transformation rules get processed. Remember this is a multi-user and multi-threaded environment.  What if multiple users are performing loads at the same time, and the rule is running concurrently for different users each with different data?

- Note that some Marketplace solutions, such as Transaction Matching (TXM) put their own TransformationEventHandler into the application, so be sure you are not interfering with that if you are using the TXM solution.