‘praeerat’ is not > pluperfect> , it is imperfective preterite, the present is ‘praesum’
(I think you meant not perfect).
My understanding of the whole imperfect/perfect thing is that the imperfect not only means something which was happening, but also something which happened habitually or continuously. Thus, the translation of an imperfect can look like a perfect as long as it’s understood that it’s a continuous state of being (see, e.g., M&F 1B.2. on the imperfect tense).
So praeerat is imperfect, but I translated this as ran because Mr. Dursley wouldn’t have merely momentarily run Grunnings. See, for example, the use of inquit throughout the translation meaning said (perfect) as opposed to an imperfect because they didn’t habitually or continuously say.
…so why isn’t fecit in the imperfect?
That’s a very good question. Maybe the sense of “made” implies that Grunnings put together, as in completed, drills – and the meaning of perfect is to complete something? That’s one rationalization, anyway!
is this book approachable after LLPSI I?
Maybe. I never got past chapter 8 or so of Lingua Latina, mostly because at that point I wanted to learn the rules and start translating rather than get them in bits. Thus, my love of M&F 
Do you have any more example of omissions/errors in Words? I’m collecting a list.
I’ve noticed the program fails to recognize the superlative in some cases; hebetissimi (dullest) comes to mind. Aside from the noun terebra, I’ve run into others over the months I’ve been using Words, but I can’t remember specific instances. I’ll remember to keep a list and occasionally post them somewhere.
BTW, if you look up inquit, Words spits out both inquiit and inquiam as entries, but if you enter either of those, Words says they are unknown.
By the way, don’t miss this detailed commentary on the Latin translation!
Wow. Just… wow.
Thanks so much for all your help. While the first three sentences took a few hours to puzzle through, the next two pages went by in a little over an hour.
–Rob