Casanova, there's 4 main factors you have to consider:
What kind of bulking/Mass Program you're on
What kind of diet you're on
How much rest between each training day you get, and how mush sleep you get per day
What kind of genetics you have
I would definitely recommend training with weights/weight machines to build mass. I would also recommend that you avoid heavy squats, which may have a slight bearing down on your spine, which at this point in time, may be just good avoidance.
You Can train squats with body weight, and do them with dumbbells at your sides.
But everything else should be fine.
When you place resistance against your bones, your bones compensate by getting thicker, hardiers, and over stronger, more dense.
So weight bearing exercise is a great thing for everyone young or old.
So get to the gym and start learning how to use the equipment there.
To get big, you have to train very very well, be very disiplined, and eat extremely well, and get the necessary rest.
If it were that easy to get a great body, huge, ripped, defined, what have you.....then everyone would have one.
So dont worry about 'I dont wanna get too big!!" notions.
You have to be COMMITED and very Disiplined to 'get big'.
As far as eating, most skinny guys simply need more calories.
When you're getting too 100s of push ups and the like, the effect of the exercise to build muscle is gone. By then its simply building your endurance, not Type 2 muscle, the Hypertrohic muscle.
So lay off such high reps on anything.
Calisthenics have a limit to muscle building. Youve obviuosly found it. Because youre not gaining from it.
Super high reps like that, and performing them every single day is THE WORST way to actually build a muscular physique. Youre just training endurance then.
Get with the weights, and dont be intimidated by them.
And lose the notion of "I dont wanna get too big!" Every beginner always says that.
I would definitely recommend a supplemental Protein powder, and Omega 3.
I also would recommend you get enough Zinc and Magnesium.
And add B Complex vitamins to the mix.
There are hundreds upon hundreds of workout programs.
Choose one, and stick to it. After several weeks, your body will often get accustomed to it, so switch to another program.
Keep eating well, make sure you GET ENOUGH Protein, and rest enough between workouts.Always try to make getting proper sleep a Priority.
Most beginners workout too much. Perform too many sets. Have bad form. Dont wait between workouts and train too often. Dont eat well. Barely get enough protein. And dont get enough water and micronutrients.
Inform yourself.
Take responsibility for informing yourself to as much of this stuff as you can.
That way you can formulate your own approach and see how your body repsonds,and what works and doesnt work for you.