POOR INTRAFAC COORD AND LCL CTLR CLEARED SMT FOR TKOF AFTER APPROVING A RWY CROSSING FOR ANOTHER SMT. FIRST SMT ABORTED TKOF.

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SMT X CALLED READY FOR TKOF FULL LENGTH RWY 1L; I TOLD HIM TO HOLD SHORT 'LNDG TFC.' WHEN THE TFC; AN SMT Z; CROSSED THE LNDG THRESHOLD I TOLD SMT X TO TAXI INTO POS AND HOLD. THE SMT Z WAS CLRED FOR STOP AND GO; BUT NEVER LANDED AND FLEW LOW OVER THE RWY. GND CTL CALLED FOR XING 1L AT BRAVO INTXN BEHIND DEPARTING TFC. I SAID CROSS 1L AT BRAVO. I THEN CLRED SMT X FOR TKOF; THE SMT Z WAS ABEAM INTXN MIKE WHICH IS THE FIRST INTXN N OF INTXN BRAVO. I DON'T REMEMBER IF I THOUGHT AT THE TIME GND MEANT THE SMT Z OR THE SMT X HOLDING FULL LENGTH REF THE CROSS BEHIND THE DEPARTING TFC. I MIGHT HAVE THOUGHT HE MEANT THE SMT X HOLDING IN POS; BUT I REALLY DON'T REMEMBER. I CLRED THE SMT X FOR TKOF AS SOON AS I WAS SURE THE SMT Z WAS IN A CLB BECAUSE IT LOOKED AS IF HE WAS GOING TO LAND TWICE; BUT NEVER DID. AS SOON AS I CLRED THE SMT X I SCANNED THE RWY AGAIN AND SAW AN SMT Y STARTING TO CROSS THE RWY AT BRAVO AND SAID HOLD SHORT TO THE SMT X; BUT THOUGHT I SAID HOLD YOUR POS. THE SMT X (PLT) SAID HE COULDN'T HOLD SHORT HE WAS ON THE RWY; AT THE SAME TIME THE SMT Y WAS ALREADY ACROSS AND I CLRED THE SMT X AGAIN. IT APPEARED THE SMT X HAD ONLY ROLLED ABOUT 500' AT THE TIME I CLRED HIM THE SECOND TIME. THE VISIBILITY WAS LOW TO THE S AND I COULDN'T SEE THE SMT X VERY WELL.