ACR FLT CREW RPTS TAXIING ACROSS HOLD SHORT LINE FOR RWY 25L AT MKE.

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WE WERE ISSUED TAXI INSTRUCTIONS THAT WERE CONFUSING SO WE BOTH WERE CONSULTING THE CHARTS AND VERIFYING THAT WE WERE TAXIING TO THE CORRECT RWY VIA THE CORRECT RTE. I WAS PURPOSELY TAXIING AT RIDICULOUSLY SLOW SPD DUE TO THE CONFUSING NATURE OF THE SURROUNDING TXWYS/HOLD SHORTS/DISPLACED THRESHOLDS/RWY INTXNS AND TAXI INSTRUCTIONS. WE BOTH COULD NOT FIND THE HOLD SHORT LINE FOR RWY 25L THOUGH WE BOTH WERE LOOKING FOR IT INTENSELY. I THINK IT PROBABLY WAS MUDDLED IN THE DISPLACED THRESHOLD MARKINGS OF RWY 13. WE WERE TAXIING ON TO RWY 25L. TWR ISSUED A STOP INSTRUCTION; BUT WE STILL HAD NOT SEEN THE HOLD SHORT LINE. WE HOWEVER STOPPED ANYWAY. A DC9 LANDED ON THE RWY WE WERE TOLD TO TAXI TO AND WE WERE CLRED INTO POS AND FOR TKOF. WHEN WE CALLED TO DISCUSS THE INCIDENT WE WERE INFORMED THAT WE MAY HAVE VIOLATED THE CLR ZONE. THIS ISN'T AN INCIDENT OF TAXIING TOO FAST OR NOT PAYING ATTN OR EVEN NOT HAVING A TAXI DIAGRAM OUT. NO MORE DUE DILIGENCE WOULD HAVE PREVENTED THIS POSSIBLE INCURSION. WE WERE ALREADY TAXIING AT THE SLOWEST POSSIBLE RATE AND STILL MAKING FORWARD PROGRESS AND WE BOTH WERE IN THE LOOP LOOKING FOR THE HOLD SHORT LINE. THIS LINE IS IN A VERY CONFUSING LOCATION AND I'M SURE THIS WILL OCCUR AGAIN AND AGAIN IN THIS LOCATION. I'M AT A LOSS AS TO WHAT TO SUGGEST TO FIX THIS OTHER THAN AVOID TAXIING ACFT DOWN THIS RWY DUE TO THE DISPLACED THRESHOLD MARKINGS AND MULTIPLE RWY MARKINGS AT THE HOLD SHORT LINE. SUPPLEMENTAL INFO FROM ACN 732501: WE WERE TAXIING TO RWY 25L. WE HELD SHORT OF RWY 19L INITIALLY TILL ALL ACFT DEPARTED RWY 25L. THEN WE RECEIVED CLRNC TO TAXI R ON RWY 13 TO HOLD SHORT OF RWY 25L. I BELIEVED WE WOULD HAVE TO CLR RWY 13 BEFORE HOLDING SHORT; NOT HAVING HELD SHORT ON A RWY BEFORE. WE HAD NOT LEFT RWY 13 WHEN THE TWR ASKED US TO STOP. THEN WE REALIZED THAT HOLD SHORT LINE FOR RWY 25L WAS BACK ON RWY 13; DEPICTED IN THE INSET; NOT THE MAIN ARPT DIAGRAM.