New member- Training Advice appreciated!

So let me start off with a bit of background. I am 19 years old and back in February of this year I was 140 lbs of mostly skin, bone, and a decent amount of lean muscle from doing a lot of long-distance running in the past. For bench I could do like 5 reps of 135, and on squats 5 reps of 185.

So around this time I started taking body-building seriously and now I about 170 lbs with all the weight gain being muscle. I haven't maxed out on lifts in a while, but now I can do 5 reps of 225 on bench and 5 of 405 on squats.

Problem is that although my workout has worked incredibly well for me, it isn't very well thought out. Five days a week since Feb. every day I've done 5x5 on bench, 5x5 on squats, then a varying mishmash of using dumbells for biceps, triceps, and shoulders, barbell calf raises, machines for back and shoulders, and then at least 10 minutes on abs. This past month I've been cutting back weight on squats due to pain in my left knee, and I feel I need to change things up because it is hard on my knee to do more than 315 on squats now and I really don't want to injure it.

I plan on doing deadlifts more because I rarely do them and don't think I work my back enough, but should I just lay off the squats for a while and do other leg excersizes? I've been thinking I should focus on different muscle groups each day as well, but I'm a dumb newbie so input from all of you would definitely help out. Avoiding knee injury is definitely the biggest priority here.

The supplements I've been using are Serious Mass protein shakes (those 1000+ calorie ones), although I've cut back on bulking with that since May to prevent stretchmarks. I also cycle on and off of N.O. Explode.

no.. you shouldn't avoid an exercise unless you're in extreme pain.  and if you ARE in pain from squatting, it's probably due to improper form.. and not going low enough.  I would bet you money that you're not doing FULL at the ground squats, and also that your form is incorrect.  i could be wrong though.

drop the weight down quite a bit, and start doing full squats.  take them REAL low.  this takes the strain off the knees when doing half squats (which are bad.. yet everyone does them haha)

throw in some deadlifts.  yes, a good benefit from doing them is for getting a stronger spine/back.  just be careful and start slowly  with low weight and ALWAYS focus on good form.   when you start to use bad form, while increasing the weight.. you're just asking for an injury eventually later on.

i do deadlifts, and squats every week.  i used to have knee pains as well, but it was due to improper squatting form.   i had to re-learn squats twice with low weight.. so just leave the ego at the door, and start all over.  you'll benefit greatly, and be so much happier when you're pain free after lifting.

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Haha you're right, I was guilty of half-squatting on high-weight sets for a while which I'm sure is the cause of the knee pain. I've been making sure to do full squats lately though and I can do that pain-free basically up to 315, but while I can do full squats of higher weight, the pain is pretty noticeable when I do and it makes me nervous. It just seems excessive to me while my knee recovers to do squats so often so maybe alternating them with deadlifts/leg press and lunges would be better?

Do you feel the pain on the other exercises? Lunges, leg press..

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a big thing is form.
like TheSilverFox said, drop the weight down...work on the form.
when you get familiar with what you're doing and build up some strength, up the weight.
and as far as other leg exercises go, you should never really abandon one part of the body in favor of the other...