Could it be faster to pitglitch here, if it works at all, instead of walking around? As it takes some time to switch items twice.
EDIT: Here's something that will save time for sure
http://dehacked.2y.net/microstorage.php/info/3662/S%26Q%20FTW.vbm
You might save time this way at more places.
Just found out that you can do it at the crocodile, not sure that it is faster though.
EDIT2: Alright! Here's my improved Bomb&Arrow route!
Overworld = 1 bombarrow (19 bombs 19 arrows) for pig.
Kanalet = 4 arrows for Bomb Enemy (15), 1 bombarrow and one arrow (18 bombs 13 arrows) for hidden knight, 2 arrows(11) for ball%chain enemy.
D3 = 3 bombs(15) for mini boss. 1 bombarrow(14 bombs 10arrows) for knightmare key. 1 bomb(13) for the clock bombs, take the bomb refills (16). One bombarrow for wall (15 bombs 9 arrows).
Overworld = Possible double bombset to kill the worm? (13 bombs)
D4 = 1 bombarrow(12 bombs 8 arrows) to blow bombblock.
D5 = New Skeleton Master fight: Do a double bomb set, slash him and let him be hit of the bombs then lay another one. You shall be able to do like that. Saving an arrow is always good:) (9 bombs). Phase 2 and 3: Lay bomb and slash him into it and lay another bomb. (5 bombs). Take the bomb refill after phase 2 (15) Phase 4: Lay bomb, slash him into it and two bombarrows.
(12 bombs and 6 arrows left.).
*No arrow refills after the Face Key*
D6 = Hit the switch, jump and take the arrows in the room with the wizzrobes (16 left).Go ahead and take the bombs on your way to the other wizzrobes (22 left). Do a double bomb set and kill the wizzrobes (20). Hookshot down, go left and kill the rabbits with a bomb (19). Double bombsetting FTW and kill the dodongos (13). Take the nightmare key, jump down and take the chest. S&Q to start. Go and kill the boss, same route as before, and same bosstactic :) (8 bombs left).
Overworld = NEW! This would be faster than switching for the arrows
http://dehacked.2y.net/microstorage.php/info/3698/Bombing.vbm. One bomb for the fire cave (7 bombs)
D8 = 1 bombarrow (6 bombs 15 arrows) for switch room. Shoot the switch with an arrow (14) 2 bombarrows (4 bombs 12 arrows) needed for walls. 1 arrow (11) for statue to get key. Go down and get the bomb and arrow refills (14 bombs 21 arrows)
D7 = 2 bombarrows (12 bombs 19 arrows) to get to the last pillar.
D4 = Three bombarrows for the fish (9 bombs and 16 arrows).
Last boss = 16 arrows (0 arrows and 9 bombs left in the end).