一般棟/二般棟/特別棟 I presume are buildings or parts of a single building which are connected by some sort of passages/walkways? (is 般 right?). I'll call them "building one", "building two" "special building". General comments - you seem to have skipped over a lot of words (保健室前と職員室前 are not even mentioned) and in some places made some weird errors which you probably would have picked up if you proofread your translation (四階建 is not "two storey", for example)
二般棟の二階から四階までは、二ヶ所ずつだ On the second to fourth floors of building two, there are two locations per floor. (6 total counted so far).
一階は保健室前と職員室前にもあるから、四ヶ所 On the first floor (of building two), since there are also locations in front of the infirmary and staff room, there are four locations. (ten total) (も binds to what it follows, so this means, in addition to the two you see on the other floors, there are _also_ locations in the named places, therefore four total)
通路の二階の、一般棟側に一ヶ所、特別棟側 に一ヶ所 On the second floor passage, there is one on the building one side, and one on the special building side. (i.e. there is a passage running between building one and the special building - twelve total)
特別棟は、各階に一ヶ所だ これで合計十六 ヶ所 In the special building, there is one per floor - that makes a total of 16 (assuming that "special" building also has four floors).
そして、階段の踊り場には全部。ということは 、一棟に二本の階段で四階建てだから、十六ヶ所か
Then, there is one on every stair landing. That is to say, since one building has two staircases and four floors, there are sixteen locations (this says nothing about passages - I'm reading 階段の踊り場には全部 as 全部の階段の踊り場にはある as otherwise it doesn't make logical sense)
I guess what you have here is two buildings with similar layouts - four stories, two staircases (one at either side), and then passages connecting the "special" building to building one. Within those buildings there are 32 total locations - 16 on the stairs, 16 on other locations. Probably this is written about a game or something where it's assumed the reader knows the layout of the buildings and just need some hints about where to look.