This is the price new boat owners pay for not getting informed on the required maintenance needed for your boat.
I believe 1 or 2 weeks ago, another new boater did the same and didn't get his boat winterized, he's having to cough up $4,000 to $6,000 for his.
Yes, this is roughly the cost to purchase the new engine, parts, and labor required to get it installed correctly. Maybe $1,000 less if you shop around and know what to look for and get, but that's it.
Keep in mind if you took a loan on this, you are going to have to get this fixed to even sell it off. Also, it might NOT be covered through your comprehensive boat insurance under your policy's fine print.
My winterization/dewinterization only costs me $120 per year, that's cheap insurance against $5,000 of parts and labor.
So in short, you are going to have to come up with $7,000 to $9,000 in parts & labor. This will be a painful but essential reminder for you to never neglect regular maintenance for your boat.
Followup:
Did you get a list of everything stated that needed to be replaced, price quotes from multiple Merc dealerships, and a second opinion from another Merc dealer or service shop? Did you also make sure the parts came with a sufficient warranty (1 year) and the installation was warrantied for a reasonable time (90 days).
Well, from your update it sounds like the replacement has already been done and paid for through financing. If this is true, stop focusing on what you might have been able to save money on and focus on properly maintaining your boat.
Call your insurance agent/company if your boat insurance policy provides coverage for this, but I would not count on it. Learn from this expensive lesson and go boating safely.