How can I combine my weight training on Mon, Wed, Fri with plyo box exercises?
Do your sprint training first, then your plyos, then your weights.
I can’t sprint train first because my school isn’t close to a track and I weightlift at my school. It isn’t ideal but it is convienient if I weight lift mon, wed, fri, and tue-linear speed, thur-change of direction, sat-agility.
When do you recover? Oh, I see that Sunday is free 
If this is your workout plan, the last thing you need to do is add in another high intensity element like plyometrics!
Don’t just add something to your program because you can do it for a reason. Plyometrics is not a magic pill and can actually do more harm than good (e.g. make you slower) if it is not integrated correctly into your programme.
Given your circumstances, you might try this schedule:
Mon.-Speed
Tues. -Weights followed by tempo
Wed.-off or just stretching (since you’ve hit the CNS two days in a row)
Thurs.-Speed
Fri.-Weights followed by tempo
With this schedule, your CNS is relatively fresh for each speed session and the tempo running will flush out the muscles after lifting. You will probably have to scale back the weights due to reisidual fatigue from the previous day’s speed work.
As far as the plyos are concerned, you might be able to do some before heading to the track for speed work. However, you’ll have to do 2 warm-ups, one for the plyos and then another one to regain warmth you lost traveling to the track.
What exactly do you intend to do with the plyo boxes? If you’re new to plyos you might just want to stick with simple hops at the track. Don’t feel compelled to use the plyo boxes just because they’re available.
Also, drop the agility crap. If you’re over 12 years old it won’t have much of a general carryover to other movements. You’re better off just practicing the specific sport/skill you want to improve.