I have to admit that my knowledge - or rather ignorance - of world championship matches is pitiful.

So I downloaded the pgn file of all; the matches from about 1880 to 1985 from the download site.

I whacked the first Capa Alekhine match game onto Shredder.

Are there any good or bad methods of engine-crunching the whole match?

Using what engine(s) on what OS? I presume the GUI is shredder about which I know next-to-nothing, I'm using Fritz 12. 

Offhand  setting any world-class engine such as Houdini, Stockfish, Firebird, Critter etc to spend as little as 5 minutes on a game will tell you (and me) way more than we'd figure out on our own, but I personally prefer to read GM annotations whenever possible and then double-check them for errors and typos using an engine

If it's Shredder from Chessbase, the GUI should be the identical with the GUI of Fritz. If it's ShredderClassic, they are very different.

You should be able to find a way to analyze the whole database at one go. I'm 100% this option was there in chessbase guis and it is likely that it would be there in Shredder Classic GUI too.

But why do you need to "engine crunch" them? For statistics?