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It's not likely to be the torque converter, Converter would cause problems in all gears and may cause engine stall when at a stop if the converter clutch was locked up, so I don't suspect the converter. I do suspect either an electrical issue or an internal transmission failure, i was thinking that it may actually be second gear, and when it gets to 3000 rpm it's actually skipping 2nd and going directly to 3rd. To verify this, I would drive it and count the shifts to see if it is actually engaging ALL gears. Let me know what you come up with on this test...
The other thing I recommend doing is having the vehicle scanned, it's possible there is still something electrical that is causing this issue, these issues will typically set a code in the TCM and it doesn't always have to turn on the check engine light. So the best thing to do at this point is to have the "Diagnostic Trouble Codes" (DTC's) read from the onboard computers. The DTC's are used as the Starting Point for diagnosis. They let you know which system(s) the fault is in. As a Technician, my first course of action is USUALLY to scan for the DTC's. Once you obtain these codes, we can more accurately and efficiently diagnose the problem and then hopefully you can make the repair. You can have these Codes read for FREE at your local auto part store (AutoZone, O'Reileys, Advanced, etc.). If you post these Diagnostic Trouble Codes here, I can obtain the most accurate information to help you diagnose the Concern, and then point you towards the correct repair.