Mooncow, the parsings you seek are as follows:
16d Def is first word; 4-letter word for a type of fish of which the first letter is the “extra” surrounded by the last two letters of a 4-letter word for small lake.
18d Def is first 2 words. “endless vacation” - remove the first and last letters & the I for Italy & the “extra” letter. You’re left with an anagram of the solution.
40a Def is retro (i.e. obs.) colour. The single word derived from the wordplay (from which you remove the “extra” letter) is Shakespearean for “to place on the sheltered side” - hence the reference to the Globe.
8d The solution is the plural of a word for the obsolete 6th letter of the ancient Greek alphabet. The wordplay is a single letter for “acceptable” in the four-letter plural of a word for vessel, of which the last letter is the “extra”.