Hi Gabe,
I can't say I know how to do this off the top of my head, but I think Automation can handle this. You probably want to check the PADS Layout Command Reference Manual but I can see some code snippets suggesting this would be possible. The Pin.TestPoint page gives the following code snippet, which removes all test points from the design and then adds one top layer test point per net on an arbitrary pin:
Sub Main
' Remove all test points
For Each nextPin In ActiveDocument.Pins
nextPin.TestPoint = ppcbTestPointNone
Next nextPin
' Add one top layer test point per net
For Each nextNet In ActiveDocument.Nets
Set arbitPin = nextNet.Pins.Item(0)
arbitPin.TestPoint = ppcbTestPointTopLayer
Next nextNet
End Sub
There is also Report Generation Language (RGL) syntax described which can report the (X,Y) location of pin & via test points, whether a net has a test point assigned, the total number of test points, etc. See the file Test Points.BAS mentioned in the document. This may be handy to check the test point locations against your ASCII list if you do end up adding them manually.
Perhaps you can add vias by (X,Y) coordinate and then set the via type to test point with the PPcbTestPointType command?