ACFT WAS DISPATCHED TO RSTRCTD ARPT WITH A 3900' RWY & NOTAMED: 3' STNDG WTR ON NORTH END OF RWY. SIGMET WAS IN EFFECT FOR MOD TO SVR TURBC BLO 10,000' DUE TO STRONG LOW LVL WND & ASSOC WNDSHEAR. CAPT MADE A SHALLOW OVRWTR APCH TO RWY 12, WHICH HAD A NR VERT 70' BLUFF SKIRTING ITS L EDGE, APRX 106' FM RWY CENTERLINE. ON FINAL APCH, CAPT NOTED VARIABLE WND CONDS & SUDDEN 15 KT INCREASE IN IAS DUE TO WNDSHEAR. HE CONTD APCH, BUT ACFT SETTLED & TOUCHED DWN 72' SHORT OF RWY. L MAIN GEAR HIT A LOG (WASHED ONTO SHORE) & LARGE ROCK, THEN COLLAPSED AFTER ACFT BOUNCED & LNDD ON RWY. UNPREDICTABLE WNDS & DWNDFTS WERE RPRTDLY PREVALENT AT THIS ARPT. OFFICIAL 1349 ADT WND WAS FM 160 DEG AT 8 KTS, BUT AT APCH END OF RWY, WND WAS RPRTD COMING OVR BLUFF & WAS GUSTY. FAA HAD GRANTED MARKAIR EXEMPTION TO OPR AT UNALASKA W/O OVRRUN/SAFETY AREAS. NO VASI AT APCH END OF RWY 12. OWNER (STATE OF ALASKA) DELAYED IMPROVEMENTS DUE TO FUNDING PRBLMS. CAPT'S 10TH LNDG AT UNALASKA; HAD NO SUNGLASSES; BLINDED BY SUNGLARE OFF WTR. REQD DRY LNDG FIELD LENGTH WAS COMPUTED TO BE 3700'.