Accong to the Z Flex liner chart I have in front of me.
6" liner can handle 213,000 BTU's at a 35' chimney height.
By code, if your water heater has a 3" hood, it can't be vented into a chimney that has more then 49 sq inches area.
If your installer read the install instructions(which I doubt), he would know that HE was suppose to verify if the chimney was sized right or not before he installed the boiler.
Draft readings would be nice.
I think you need another contractor.
Screen them on the phone. Let them know them problems your having, so they can bow out gracefully if they don't know how to check everything.