Hi, xij:
3a: PEA is an obsolete term for peafowl (“bird dropped”) + T for “tons”. You need to change the last letter before entry to give an item of food.
13a: “rout” can mean “herd”, so “leaderless herds” gives OUTS; “deep” can mean “most still”, so “most still going west” gives PEED.
45a: I struggled to make sense of this until I noticed that the second, third and fifth letters (the ones in “prime locations” as in prime numbers) of “holes”, when rearranged (“bothered”, give SLO + W (“wife”). You need to change the third letter before entry to give an item of food.
35d: “Spent” contains a misprinted letter, and should read “scent”. An obsolete meaning of “train” is “to allure”, so “mostly to allure, not now though” gives TRAI + L for “ladies at first”.