You might want to give more details. What Year/model is your engine?
What work did you actually have done?
You say, "the machine shop removed the bolts I had left in" does this mean you took the engine to a shop? Did they have the whole car? What work did they perform exactly?
What were the symptoms that lead you to repair the engine in the first place?
By "water bottle" do you mean the radiator or the coolant overflow bottle? Saying that you filled the water bottle from both sides suggests the radiator, but is that what you meant?
Did you fill the engine with coolant after the HG job or did the shop do it?
This board is great for getting answers to your questions, but it is REALLY important that you give as much of the facts surrounding your problem that you can so that the board can answer your questions accurately.
Sure, its an '98 OBW with 224k miles on it (EJ25D).
The initial symptoms I had (last year) were small bubbles in the overflow tank and overheating on long journeys. The over heats got more frequent and more and more water started getting pushed into the (overflow) bottle. It got to the point wher I could only drive 2 miles before overheating.
I bought the engine re-seal kit and started work on replacing the HGs 3 months ago. I got the heads off and gave them to a machine shop to recondition. After 3 weeks I got them back and continued with my job.
I finally got the engine back in and started it for the first time Sunday.
I filled it with water and burped it once (filled rad with water/coolant from main inlet and from vent plug hole (passenger side)). When water came out of vent side during filling from main inlet I replaced cap and vent plug.
Drove car to work today and repeated vent/main inlet refilling procedure when I got home.