ACR RECEIVES PRE DEP CLRNC VERY LATE. ENTER WRONG ALT IN ALT ALERT WINDOW. TCASII TA.

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DURING PREFLT ACTIVITIES; THE ALT ALERTER WAS INADVERTENTLY SET TO 5000 FT AS INITIAL LEVEL OFF ALT. THE PDC (PRE DEP CLRNC) CAME VERY LATE; JUST PRIOR TO PUSHBACK VIA THE ACFT ACARS PRINTER. DUE TO ITS ARR AT PUSHBACK; A VERY BUSY TIME; WITHHELD CHKLIST ITEMS WERE COMPLETED. 'TRANSPONDER'; WHICH I REMEMBER XCHKING AGAINST THE PDC; AND 'NAV RADIOS' WHICH THE INITIAL RTING OF THE IAH 338 DEG RADIAL I ALSO REMEMBER XCHKING WITH THE PDC; HOWEVER; I ALSO RESPONDED WITH 5000 FT BY REF TO THE ALT ALERTER; NOT XCHKING IT AGAINST THE PDC! HERE WAS OUR PROBLEM. OUR CLRNC WAS ONLY TO 4000 FT. THE TKOF BRIEFING AT THE END OF THE RWY WAS 'RWY HDG TO MAINTAIN 5000 FT' SHORTLY AFTER TKOF WHILE IN A LARGE L TURN THE FO NOTED AN ACFT APPROX 1200 FT ABOVE US IN OUR CLB PATH. (TCASII EQUIPPED ACFT AND THERE WAS A LOT OF WX IN THE AREA). BY THE TIME THE FO ADVISED ME; THEN TOLD THE TWR OF A POSSIBLE CONFLICT; (MENTIONING LESS THAN 1000 VERT SEPARATION) OUR TCASII GAVE A TA; HAVING REDUCED THE RATE OF CLB AS THE SITUATION DEVELOPED; I (PF) IMMEDIATELY LEVELED THE ACFT. AT THIS SAME TIME THE TWR TOLD US 'MAINTAIN 4000 FT.' BEING AT 4300 FT WE DSNDED TO 4000 STATING WE HAD NOT CONFIRMED 4000 FT EARLIER. AT THIS TIME WE LEARNED OF OUR ERROR. AFTER LENGTHY CHKS; REVIEWING THE SID; AND FLT PAPERS; NEITHER THE FO NOR I CAN DETERMINE WHEN 5000 WAS SET INTO THE ALT ALERT. WE DO KNOW THAT TIME WAS SHORT WHEN WE RETURNED TO THE COCKPIT. TURN-AROUND TIME WAS QUICK; THERE WAS A LOT OF WX ALONG THE IAH-DFW RTE AND DELAYS GOING INTO DFW. UPON COCKPIT PREPARATION; THERE WAS THE LATE PDC; COMING AT PUSHBACK; A PERIOD OF DUTY SATURATION! BUT; NOT A TIME TO RUSH. IT IS PROBABLY DURING THIS BUSY TIME PERIOD THAT 5000 FT WAS INADVERTENTLY SET; OR THAT POSSIBLY IT WAS NOT RESET FROM THE ARR CLEANUP. CONTRIBUTING FACTORS MIGHT BE THAT THIS WAS OCCURRING DURING THE LAST LEG OF A DAY FLYING 8 HRS; 11 1/2 HRS AFTER HOTEL PICK UP. ALSO THE LACK OF ANY GUIDANCE FROM THE SID. NEITHER A PUBLISHED ALT; NOR ANY NAVIGATIONAL PROC. IT IS MY DUTY TO CHK THE ALT SET IN THE ALT ALERT DURING THE PREFLT CHKLIST. IT IS THE CORRECT AND EFFECTIVE PROC THAT BOTH THE FO AND MYSELF FAILED TO XCHK THE ASSIGNED ALT. A REMINDER FROM THE TWR AS PART OF THE NORMAL CLRNC DURING TKOF MIGHT BE HELPFUL. I.E. 'CLRED FOR TKOF; MAINTAIN RWY HDG AND 4000 FT'. ALSO A MORE TIMELY CHANGE TO DEP; AS WHEN SWITCHING FREQS THE ALT LEAVING AND ALT CLBING/DSNDING TO ARE ANNOUNCED. I CAN ONLY SAY THAT AN ALERT FO WHO PROVIDED VERY TIMELY INFO TO BOTH ME AND THE CTLR; PREVENTED A VERY POTENTIALLY ACCIDENT. THE TCASII TOO WAS MOST HELPFUL; AS IT PROVIDED THE INFO AND PROBABLY WOULD HAVE FOLLOWED WITH AN 'RA' TO US HAD WE NOT STOPPED OUR ASCENT. SUPPLEMENTAL INFO FROM ACR 199611: ADDITIONALLY; HAD THERE BEEN A MORE EXPEDITIOUS HDOF TO DEP (3 MINS 29 SECONDS IN IMC); WE WOULD HAVE CHKED IN WITH DEP; RPTED CLBING TO 5000 FT WHICH WOULD HAVE BEEN ANOTHER XCHK THAT MAY HAVE PREVENTED THIS INCIDENT FROM OCCURRING. I FEEL AN ALT ON THE TKOF CLRNC (ESPECIALLY WITH NO EXPECT ALT ON THE SID IN A DATA LINK CLRNC DELIVERY ENVIRONMENT) WOULD BE AN ADDITIONAL SAFETY MEASURE.