The wastegates are seeing direct boost pressure, as in the boost solenoid is bypassing. The same thing happens with the boost controller turned off. Is it possible you did not replace the vacuum lines going to the boost solenoid as they were before? Or perhaps the boost solenoid wiring repair was not done properly? Or like you said the boost controller could have been damaged if the control wires for the boost solenoid were shorted. Take some photos of your boost controller solenoid setup. How are the vacuum lines routed?
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