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Swimming is always a good thing especially for the spine so you are good to go.

it's normal absolutely yet your left side strength and muscles and those right should not differ significantly.
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less weight - more reps... no 1 rep lifts!

If it's post workout muscle soreness that's ok. I dont think it's tendonitis. It could be just muscle/tendon strain. Just take a week off and see if it goes away. Take fish oil and...

it's not uncommon... just add joint supps and fish oil to your daily supps.

Could be just tendon/nerve strain. Sometimes I feel the same way when I do PULL DOWNS, yet this feeling disappears within 1 to 3 days. Anyway go see your ortho.

stop doing deads and squats for a couple of weeks and see how it goes.

nothing to worry about... but have your doc look at it anyway. BTW do you eat much salt?

Glucosamin/Chondroitin/Hyaluronic Acid supps daily (similar to SCHIFF Move Free) + fish oil. Take Aleve if needed (painkiller):

http://buygenericsguide.com/buy-aleve/

Report back in 2 weeks.

I strongly recommend you guys take glucosamine/chondroitin supps. You can also add Hyaluronic Acid, Vitamin D, fish oil, and you may need to take Aleve to deal with pain:
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I also used to take Aleve:

http://buygenericsguide.com/buy-aleve/

I strongly recommend you take hyaluronic acid based joint supps similar to WEIDER/SCHIFF Move Free (hyaluronic acid, glucosamine, chondroitin) plus MSM and vitamin D and fish oil
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looks like crap to me ... I'd prefer UN Glucosamine/Chondroitin/MSM supp anyway

intense warm up before workout

Sounds like joint wear... Go see a doc and try taking glucosamine/chondroitin supps.

If you still want to train take joint supps those with Chondroitin, Glucosamine, MSM and Hyaluronic Acid:
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That's more safe for your joints, however some extra forced reps are essential to increase strength. Including joint supps in your daily stack will help you avoid problems with your joints in future.

Do you take joint supps?

What hernia is it? If it's inguinal hernia you can still train but not so hard, just avoid exercises that cause pain. A friend of mine was already in gym a month after surgery.

A couple of weeks off would be wise. Second, go see an ortho so he could examine your neck, shoulders and back.

Aleve usually helps me with moderate to severe neck pain. I bought it from here:
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Could be joint pain. What joint supps do you take?