Drupal Commerce Rules if Paypal Payment Method is Selected
You can use the event

'After updating an existing commerce order'


on condition 

'Selected payment method comparison' under commerce Payment and select its value to 'Paypal'

Now in action add 'Remove taxes applied to a line item' and another action 'Add an item to list' to add %3 amount to total .

It will perform accordingly.

Hope it will work for you!