The stock gift module and the pledge module were not designed to work together. There is a series of steps you can follow that should allow you to connect up a stock gift to a pledge payment. The document is attached. It would be best to run through the procedure several times in your test database until you feel comfortable doing it.
An alternative to the documented method is to process the stock gift normally and then process a pledge payment. This will result in an extra gift, but journals can be processed to manipulate the general ledger.