5/3/1 and cardio.

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I know jims a big proponent of tire flipping and hill climbs with weighted vests but it's cold out and I have unlimited space to do these things anyway. I saw wendler has made some suggestions for metcon training indoors; I did a jump rope metcon that he created today and it was awful. What confuses me about this though is it sounds like he wants you to do his metcons immediately after doing main lift work and one accessory exercise. Is it ok to do metcon work by itself? I know Jim is pretty adamant that people don't customize with his program, but I would honestly prefer to do conditioning work or cardio on a day other than when I'm focusing on main lifts.