Holy shit man that is scary! Glad you at least figured it out.
Now, here is what I do know. In 100% of the hot water tanks (that I have seen) the HVAC blower is NOWHERE NEAR THE HW FLUE! So that like yeah I was putting new tires on your car but somehow drained all the oil out, oops my bad :)
As far as the first company, I would demand my money back AND dispute all charges. I would investigate legal action. What those guys did was incredibly dangerous. If you had not been the responsible party here (CO detectors) horrible things could have happened.
To use the car analogy again, if you dont know how to change brakes on a car, maybe you should not do it? Because the consequences of getting in wrong can be deadly!