On non-grappling days, I like to do do alot of functional training too:

Regarding body weight workouts: - Burpees - Jump Rope - Body weight squats - Pushups - Pullups (would love to do this, but haven't installed a bar yet)

I also really like to swing the kettle bells. I have a 60 lb kettle bell that I like to do 2 handed kettle bell swings with.

A work out that destroys me is doing Tabata intervals, alternating between kb swings and burpees. It works out the entire body and gets the heart rate up in no time.

Areas I think I can improve are increasing my flexibility (hips are tight and make certain movements difficult), and I plan on doing some Yoga and Ginastica Naturale movements... (again implementing this has been the hardest for me since when I have time MY primary focus is honing BJJ technique and body recomposition)

I don't pretend to be an expert, but I also do BJJ and my favorite bodyweight workout is:

Round A (each exercise 1 minute): leg lifts, dips, squat jumps, planks, lunges Round B (each exercise 1 minute): leg lifts, push-ups, burpees, supermans, lunges

Alternate Round A and B for however many rounds you want to do; I usually do 5 (so ABABA) with no rest in between but YMMV. If I can find the one jumprope in the gym, I sometimes replace the squat jumps with that.

I like it because it's short and sweet; I'd rather spend 25 minutes of hard work and get on with my life than take 1 hour and half-ass it the whole time. I think it really helps my conditioning for rolling, and it's pretty flexible if you want to replace anything.

What are your goals? I don't understand the need for all this extra bodyweight work. 1-3 hours of BJJ every day should be giving you plenty of your-body and other-people's-body conditioning work.

If you want to lose weight (from skinnyfat to skinny?), you're probably better off focusing on diet and sleep. 1-3 hours a day of BJJ is already a good amount of work, why add a bunch of lifting and running to it? Seems like a recipe for overtraining to me.

If your goal is functional strength, is grappling strength not best built through grappling?

My second choice would be properly executed barbell training. I'm talking about big compound movements from Starting Strength - squat, deadlift, overhead press bench press, and power clean.

I'm still learning but my goals are also MMA technique, functional strength, and body recomposition.

I think that there are some great responses here, but the answer to your question might be a synthesis of them all;

It seems that your goals are, broadly speaking, functional strength and overall body conditioning - presumably, to aid in your BJJ sparring (as well as being an end in itself).

As some of the posters have mentioned, squats, deadlifts, presses, kettlebells, etc. - weights - which are a great option. However, you specifically mentioned calisthenics, which I think is an excellent idea for BJJ training.

Personally, I would drop the situps, forearm curls, and possibly leg raises. In terms of core training, situps/crunches are completely useless isolation exercises - I would recommend that you begin training L-Holds, levers (front & back) and flags. Not only are these full body isometric exercises, they completely beat both leg raises and situps/crunches in terms of core strength. Additionally, rather than doing forearm curls, I would recommend training fingertip pushups in conjunction towel-pullups and/or rope climbs. All three will improve your grip and forearm strength much more effectively and in a much more balanced way than any curl ever could. In addition to dips and pullups/chinups, it would be worthwhile to work on handstand pushups and muscle-ups. Both will improve your total-body strength and coordination, as well as being unbelievable exercises for grappling.

I also think that it would be wise to sprint, rather than run if you so choose to at all. My instinct says that you'll be at risk of overtraining on a schedule like this, but you'll know your own body better than anybody. If you can spare the time and recovery, then add in sprints - in general, they're more effective for aerobic and anaerobic conditioning than running. Otherwise, I would advise you to focus on bodyweight work and BJJ, and if you need the high-intensity (which would otherwise be provided by running/sprinting) then do your bodyweight work double-time (read: 150% intensity).

Here are some articles you might find interesting:

Sprinting: https://www.marksdailyapple.com/why-we-dont-sprint-anymore-plus-a-primal-health-challenge/

Human Flag: http://www.alkavadlo.com/2010/03/15/all-about-the-human-flag-part-one/

Handstand-Pushups: http://www.crossfitlondon.ca/wp/zero-to-10-handstand-pushups-hspu/

Muscle-Ups: http://www.alkavadlo.com/2011/02/16/getting-your-first-muscle-up/

There's a whole plethora of resources, but here's a starting point. Keep us posted with your progress and workouts!