The general rule of thumb with regards to exercise order is to start with the larger muscle groups and end with the smallest in full body or any other exercise scheme. So it would be legs, back, chest, shoulders and arms. You want a flow from one major muscle group to another in this style of training. The smaller groups, calf's & abs,are usually considered auxiliary units. They can be done at the end of the total body workout or thrown in at selected points in the program. Like squats, ham's & calf's for lower body. Back with abs.
With proper martial training anyone should gather quickness & speed from just those type's of workout's during dojo time. If not, your teacher is not complete in his training methods. Jumping squats with weights are not needed. One good reason for not doing them is risk of injury. Regular squats are a prime movement to increase the jumping abilities of anyone. Remember that increasing strength will also increase speed & quickness.
If you really want to increase your jumping you can try holding a broom handle down and in front of you body. Now jump over that handle, landing with the broom handle in back of you. Return to the original position by jumping back over the broom handle again. Must lift the knee's extremly high & fast to clear the handle. Not only great for the calf/legs/hip strength but outstanding for the abs. Also a very good stamina builder. A lot of men will use a load BB rather than something like a light broom handle for these jumps. A Olympic bar with the basic 135lbs on it is a common starting point for a lot of athletes.
Far as a full body lifting program goes you might try something like this:
Squat...quads/hips
SLDL...ham's...don't need to go too heavy...Straight back & work for the stretch/feel
Chins or rows
Hi-Pulls or cleans
Dips or inclines
Military press or PBN
BB curls
Feel free to throw in calfs or abs if you wish, where ever you wish. If it's that important to you.
Two set's each of 6-9 reps for power development. Twice a week. If you think you can handle more sets and still make progress than do 3 sets each of the same rep pattern of 6-9 reps. You can only be the judge. Good Luck.