Looks like that housing was definitely ported for an external wastegated downpipe. Either get Jason at RJCs plate or buy a new turbine housing. #2, the stock wastegate actuator will not bolt up to a TE series turbo (which obviously you just found out the hard way.) Either purchase a new standard or heavy duty spring wastegate that is specific for TE series turbos from PTE or, or use one of you backing plate brackets that is on the turbo and weld it to your stock actuator once you have it aligned properly. The only difference between a standard springed wastegate actuator and a heavy duty actuator (if both are for the same turbo) is the internal spring in the Heavy duty is stronger. If you decide purchase a new turbine housing from PTE, you will need this part number, THB3-31. (That is if your turbo is a TE-44 that was built by either PTE or Limit Engineering) Going with the plate method will space your downpipe further away by the thickness of the flange, this might cause some issues with a stone stock wastegate elbow assembly. If you do decide to get a 3" Terry Houston style downpipe, it completely replaces the stock cast iron elbow. Typically, people port the wastegate hole on the turbine housing out to 1.20" - 1.25", anything larger is typically for an external wastegate setup.
Hope this helps.
Patrick