Do 5/3/1 as written, then follow it up with a met con as a finisher. Modify the met con so that it's lower body specific on lower body 5/3/1 days and upper body specific on upper body 5/3/1 days. This setup works best when 5/3/1 is done as a 4 day split.
If you want to keep the random met con or follow someone else's CF programming it'll impact your ability to progress on strength and possibly increase your potential for injury... so you're going to have to make a decision about which is more important to you and make intelligent programming decisions as appropriate.
When I did Boring but big I Super-setted my assistance work, and tried to perform the 50 reps of both exercises as fast as possible with as little rest as possible in between sets, which usually didn't take more than a few minutes; obviously my form took priority over my speed of execution. Hill Sprints, Jump rope, and Prowler pushes are often recommended 3-4x a week whenever you can fit them in basically.
I'm lucky enough to live next to a beach, so I spend about 10 minutes sprinting through the dunes, trying to beat my distance each time. rock climbing feels great too. Find a rock, or a wall, or a tree, and ascend it rapidly yet safely. do either of these for 10-15 minutes with enough effort and your conditioning will be pretty solid. I also jumped rope between my 531 sets.
I believe Jim has a section in the 2nd Edition called "5/3/1 and Crossfit." He gives ideas on how to setup your "Crossfit" style template. Not going to give too much detail but you start with your 5/3/1 Lift, your big assistance lift, then move on to your met-con style training. He then goes on to list many examples and different movements you can do to get everything setup appropriately.
Your current level. Your current conditioning goal (performance/consistency) Your strength goal.
Once you understand and answer these questions, all things make sense. The problem is people trying to combine a well-structured training program (strength/speed/agility/recovery/mobility/flexibility) with a random conditioning program. I don't think anyone really believes in just throwing shit against the wall is a good way to succeed - its not even up for debate. So address the easy-to-answer questions above and you will know exactly what to do. But until you can accurately know your goals for the six week session and the training year, how can you program anything?
I decided to super set or circuit set my assistance work, depending on the day. All 5/3/1 core lifts remain exactly as prescribed in Jim's book, but I kept the two assistance exercises and added 1-2 more assistance exercises to my template, doing them in strict circuit form as opposed to straight sets, and lowering rest intervals. In addition, on off days, I am using the "Couch to 5k / C25K" app, which is free for Droid or ioS, which involves sprint intervals OR I will do stadium or hill sprints here at the local high school track, following Jim's recommendations outlined in his conditioning protocols that were published on T-Nation and in the Beyond e-book.
Here's an example of what I did yesterday:
Core lift, Week #2, Cycle IV / Bench Press (3/3/3+/FSL as many reps as possible) - 140 x 1 x 3, 160 x 1 x 3, 180 x 1 x 5, 140 x 1 x 18 (AMRAP / FSL)
Assistance work = circuit sets, A1-A4, 45 sec. rest between each exercise, 90-120 sec. rest between full circuits, 5 circuits total completed. A1 and A2 are my standard assistance exercises following Jim's stock triumvirate template. I've added A3 and A4 for extra conditioning this cycle, using weights that do NOT impeded my recovery on the 4 core lifts.
A1. Incline Barbell Bench Press - 95 lb x 5 x 10 A2. One-arm DB rows - 65 lb x 5 x 10, each arm A3. Kettlebell swings - 25 lb x 5 x 25 (25 lbs is the largest available to me, so aimed for more reps) A4. 20 yard walking lunges - 25 lb x 5 sets @ 20 yards per set
Lactate conditioning immediately after my workout above: 400 meter sprints on school track, 2 full sets, 3 min rest between sets. Again, these are just a couple of finishing sprints to get my heart rate elevated, but I'm not so sore that it impedes my progress on lower body work.
Goal - lose 8-10 lbs of fat, maintain or increase strength on core lifts, and be able to run 2.5-3 miles in less than 8 min/mi.