Pictures? How can we know what you're talking about without them?

Pictures don't show the color too well.

before poly. It was ash brown.became very deep brown with red and orange spots

You're fighting Mother Nature. It is the nature of oak to do exactly that. Your installer should have shown you complete examples with the finish included. The finish will always darken and richen the wood. And it looks just fine. It isn't "red" at all.

Can he buff out he first coat of poly and do a thin coat of stain and then finish with water based poly?

I'd ask the question in the flooring forum.

Stain does not penetrate finished wood. It must be raw wood. A tinted clear coat can ''tone'' wood, but will show color change as it wears off. It will also mask grain.

Water based sealers change the color less than oil based. You can't sand off the sealer without effecting the stain below. Back to raw, or close, if the color is that important.

Sophie how do you tint clear coat? Do you mean adding some stain to poly?

Can the floor be sanded lightly to remove the poly, so it can be stained again?

Sophie, when you say tinted, do you mean just adding stain to poly?

when I look at the floor away from the sun it doesn't look too bad, but where the sun hits it it looks orange. is this usually the case unless floors are extremely dark? I would redo, but there is no guarantee I will get the color right. the only way to achieve a more uniform color is with two coats of stain, which is not recommended because of poly issues, which I already had with this floor. this floor doesn't absorb stain well and takes a long time to dry, do two coats of stain is risky. we r way behind schedule. is this floor acceptable? I guess at this point I am completely confused and just looking for honest opinions. btw it still needs two coats of poly, so I am hoping it will improve once finished. thanks!

I think its lovely! Not orange. Just warm, and isnt that what we want our homes to be?

Tell us the full name of the varnish used. Most will slightly darken any wood and make it a little warmer. Your finisher should have told you that. All the finishers I know provide a finish sample in order to avoid such problems.