ALTDEV ALT OVERSHOT IN MDT.

Narrative

APPROX XX25 LCL WE TOOK OFF FROM PNE TO JFK. IT WAS TO BE A FERRY FLT. AFTER LIFTOFF FO RAISED THE GEAR; HOWEVER; THE L MAIN GEAR WOULD NOT STAY UP AND LOCKED AND KEPT RECYCLING. I WAS FLYING THE ACFT AND TOLD THE FO TO RECYCLE THE GEAR. THAT DIDN'T WORK AND I LEVELED THE ACFT AT 3000 FT AND PUT THE AUTOPLT ON. I TOLD THE FO TO FLY THE ACFT AND COVER #1 RADIO AND WOULD TAKE CARE OF THE PROB. I LET THE FO KNOW IT WAS ON THE AUTOPLT BUT I FAILED TO MENTION IT WAS COUPLED TO MY SIDE. I SWITCHED OVER TO #2 RADIO TO TALK TO MAINT. MAINT HAD ME RECYCLE THE GEAR AND RESET THE GEAR CIRCUIT BREAKER. MY ATTN HAD BEEN DIVERTED DOING THOSE THINGS. WHEN I RETURNED MY ATTN TO THE ALTIMETER I NOTICED WE HAD CLBED TO 3600 FT. AT THE SAME TIME PHL APCH QUESTIONED OUR ALT. THE FO WHO; TRYING TO FLY THE ACFT WITH AUTOPLT; FINALLY PUNCHED IT OFF AND RETURNED TO 3000 FT. SOMETHING HAPPENED TO AUTOPLT WHERE FOR SOME REASON IT DIDN'T COUPLE WITH ALT HOLD. THE GEAR PROB COULD NOT BE RESOLVED AND WE RETURNED TO PNE WITHOUT FURTHER INCIDENT. 3 THINGS MAY HAVE CAUSED THE PROB: MY TURNING OVER THE ACFT WITH AUTOPLT ON AND NOT MAKING SURE THE AUTOPLT HAD CAPTURED ALT AND HDG. NEXT TIME PUT AUTOPLT SELECT TO PF ACFT. MAKE SURE PF THE ACFT IS DOING JUST THAT NO MATTER WHAT CONFUSION OR PROB GOING ON ELSEWHERE. SUPPLEMENTAL INFO FROM ACN 247748: AFTER TKOF WHEN THE GEAR WAS RETRACTED; THERE WAS A LOUD THUMPING NOISE IN THE COCKPIT; CAUSED BY THE GEAR NOT BEING STOWED PROPERLY IN THE WHEEL WELL. THE CAPT AND PF PLACED THE ACFT ON AUTOPLT AND TURNED THE ACFT OVER TO ME; THE PNF. IN THE TRANSITION THE ALT HOLD WAS INADVERTENTLY KNOCKED OFF AND THE ACFT STARTED TO CLB AT A RAPID RATE. WITH THE ENSUING CONFUSION OF THE THUMPING GEAR; THE ALT DEVIATED 400 TO 600 FT BEFORE I WAS ABLE TO SWITCH AUTOPLT-FLT DIRECTOR SYS AND PUT THE ACFT BACK ON THE PROPER ALT. WE MIGHT HAVE SLOWED DOWN IN THE TRANSITION; ALTHOUGH IT'S HARD WITH OUTSIDE NOISE CAUSED BY THE GEAR.