Hi and welcome - oh my this poor little baby! Being sold at a pet store when it shouldn't even have been taken from its Momma for another 5 weeks - that's very dangerous.
Well, firstly, please don't ever buy from a pet store again - they are *incredibly* unscrupulous and will do/say anything to sell their "product". The fact they even accepted a 7 wk old sick puppy AND sold it you should tell you exactly who they are as far as values. This puppy very likely came from a puppy mill, btw, bc that's where most pet stores get their animals. This means you're supporting puppy mills, even though you didn't mean to...so keep that in mind too. Don't get down on yourself though, please, bc we've all made mistakes w/ dogs - believe me!!
On to this poor little one. As far as keeping him, totally up to you. I'd have his knees checked asap for having early LP - but even if he doesn't yet have it, just know he could. As far as the murmur, yes, could easily outgrow this so that's not the biggest deal. Coccidia is not uncommon in pups. And as far as the neuter - it will def not take 2 surgeries - one should be just fine - it's just that the surgery is more similar to a spay in that they have to go in the abdomen to find and remove that undescended testicle.
The pet store should be paying for ALL of this, btw. I'd be pretty furious if I were you
. Best of luck and do keep us posted!