PLT OF BE200 MISSES PART OF AN AMENDED DEP CLRNC AND CLBS ABOVE ASSIGNED ALT. LTSS RESULTS.

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MAINTAIN 5000 FT. AS I WAS TAXIING; GND CALLED AND CHANGED THE CLRNC TO: NOW CLRED VIA THE TYGER 3 ARR; MAINTAIN 5000 FT. I WAS FLYING SINGLE PLT SO I WAS PERFORMING THE CHKLIST ITEMS MYSELF. I CALLED THE TWR AND TOLD THEM I WAS READY FOR TKOF. THEY CLRED ME FOR TKOF AND ALSO GAVE ME NEW DEP INSTRUCTIONS: TURN R TO A HDG OF 340 DEGS AND MAINTAIN 3000 FT. I WAS AGAIN PERFORMING THE 'FINAL ITEMS' CHKLIST WHILE TAXIING ONTO THE RWY. WHILE DOING THIS; I READ BACK THE INSTRUCTIONS AND STARTED MY TKOF ROLL. EVIDENTLY I READ BACK CORRECTLY BUT FAILED TO DIAL IN 3000 FT INSTEAD OF 5000 FT IN MY ALT ALERTER. I SPOKE THE WORDS; BUT IT JUST DID NOT 'CLICK' WITH ME THAT THIS WAS A DIFFERENT ALT THAN MY CLRNC (ORIGINAL). I DEPARTED; TURNED TO 340 DEGS AND CONTINUED CLBING. PASSING 3000 FT; I SPOTTED A COMMUTER PLANE AT MY 10 O'CLOCK POS ABOVE ME TRAVELING L TO R. I PASSED APPROX 1000 FT BELOW HIM; SO NO EVASIVE ACTION WAS NEEDED. I THOUGHT IT ODD; THOUGH; THAT THE TWR DID NOT INFORM ME OF TFC. I CONTINUED TO CLB TO 5000 FT (STILL SET IN THE ALERTER). AT NO TIME DID THE TWR INFORM ME THAT I HAD GONE THROUGH MY NEW ASSIGNED ALT OF 3000 FT. AS I WAS LEVELING AT 5000 FT; THE TWR HANDED ME OFF TO DEP CTL. STILL NOTHING WAS SAID BY TWR ABOUT MY ALT. ONLY THEN DID DEP QUESTION ME ABOUT MY ALT ASSIGNMENT. STILL NOT REALIZING MY ERROR; I ANSWERED '5000 FT.' SHE SAID 'OK' AND THE FLT CONTINUED NORMALLY. ENRTE; I WAS ASKED BY ZKC TO GIVE SGF TWR A CALL WHEN ON THE GND. ALTHOUGH I HAD NO IDEA WHY I WAS ASKED TO CALL; I DID SO AND IT WAS THEN I WAS INFORMED OF WHAT I HAD DONE.