PLT OF A PIPER PA30 TWIN COMMANCHE OVERSHOT DEP ALT RESULTING IN A CONFLICT WITH OTHER ACFT. THE PLT BLAMES THIS INCIDENT ON ATC GIVING A LATE CLRNC TO STOP CLB AT THE ALT PASSING THROUGH AND AUTOPLT SLOW IN RESPONDING TO A DSCNT BACK DOWN TO THE NEWLY ASSIGNED ALT. RPTR DISENGAGED THE AUTOPLT AND RETURNED QUICKLY TO ASSIGNED ALT.

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I DEPARTED RAL IFR TO VFR ON TOP IN 4 MI VISIBILITY 3000- 3500 FT OVCST WITH TOPS AT 5000 FT AT APPROX XA45. I DEPARTED ON RWY 27 DIRECT TO PDZ VOR WITH A CLRNC TO MAINTAIN 4000 FT AGL. I WAS HANDED OFF TO SOCAL APCH FROM RAL TWR. AT ABOUT 1500-2000 FT I WAS DIRECTED BY SOCAL APCH OR VECTORED OFF MY DIRECT HEADING TO PDZ VOR APPROX 2 MI PRIOR TO THE FIX BY SOCAL APCH AND TOLD TO TURN TO A HDG OF 140 DEGS WHICH I DID AND CLB AND MAINTAIN 4000 FT. AS I WAS COMING UP THROUGH 3000 FT I WAS AMENDED TO MAINTAIN 3000 FT; I HAD AUTOPLT SET FOR 4000 FT. BY THE TIME I REACHED THE KNOB TO RESET TO 3000 FT AND SET PITCH FOR DSCNT I WAS CLBING THROUGH 3600 FT. THE ACFT DID NOT RESPOND QUICK ENOUGH SO I TURNED OFF AUTOPLT WHEN APCH ANNOUNCED TFC ALERT 12 O'CLOCK POS. APPROX 3 SECONDS LATER I WAS AT 3000 FT WITH MANUAL CTL AND I HEARD ACFT AT 12 O'CLOCK POS ANNOUNCED. HE WAS IMC WHEN I WAS VFR AT 3000 FT. I WAS TOLD TO CALL 619 AREA WHEN I LANDED WHICH I DID AT CALEXICO. NOTE: I BELIEVE THE CTLR SHOULD HAVE LET ME CONTINUE TO PDZ VOR AS WAS INITIAL CLRNC AND NOT VECTOR ME INTO A 12 O'CLOCK POS ON-COMING ACFT. THE TFC ALERT WAS GIVEN WITHIN 30 SECONDS AFTER VECTORING ME IN HIS DIRECTION.