"coiner" - one who counterfeits coins. Not something we hear of much today, but in earlier times was a reasonably familiar sort of criminal.
"box-room" - a room in a house (usually a small room) which is just used for storing things, usually things that are not wanted very often. The collocation "box-room attic" is unusual, because these two words mean nearly the same thing. (Not quite, because a box-room could be anywhere in a house, not just under the roof).
"cistern": yes, it is still quite common for British houses to have a water-tank in the roof space - sometimes two (hot and cold). This was partly to provide a head of pressure for taps and showers, and partly to guard against interruptions in supply (and in the case of hot tanks, to provide a reservoir of heated water for when you needed it quickly, as in a bath).
There is not a literal tunnel, it is saying that between the tank and the sloping roof there is a long and narrow dark place (dark because it is behind the cistern).
"of course" is a parenthetical remark meaning "as you already know", or "as is obvious". It is much more common in speech than in writing, but of course this writing is meant to suggest somebody is speaking, and telling a story.
"For" says that the sentence is a reason or explanation of what precedes. So the meaning of "For of course he was thinking .. " is something like "(He was excited) because, as you probably realise, he was thinking ... "
Best Answer
The observation behind this question is very nice. Use of this locution in indeed limited, to perfect tenses:
You can clearly imagine putting the phrase into other tenses. For instance, by analogy of I have been silly to I am (being) silly, you could form *I am to London, *I am being to London. Similarly, you expect *I was to London (I was silly) and *I will be to London (I will be silly). But none of these are possible.
Note 1. It is wrong to think of to have been as having have as a main verb. If so, one would expect the possibility of the past perfect have had been (comparing to, say, have had it coming), and this is clearly impossible.
Note 2. There is a (rather outmoded English?) idiom to have been, without any destination/location specified. It is a euphemism for going to the toilet. Monty Python made a recurrent joke out of it in a skit based around an Agatha-Christie-style murder (the reluctance to say murdered led to numerous characters asking simply Has he been ... ?, to which the others would answer something like Yes, before lunch).