Renovation... nothin like a last minute stain emergency

Just when you think it's smooth sailing some crazy thing comes up and bites you in the a**.
All along I had dreams of floors that looked like this...
Problem #1
We pulled up the old oak strip flooring that was on half of the floors and planned on sanding off the paint that was everywhere else.  We ordered new wood to replace the spots that had previously had the old stair, old kitchen linoleum and a few other odd bits.  We made the wood decision based on a fair amount of guesswork as we couldn't see most of what the wood was - Super, crazy big mistake!
As the floors were sanded we started to see what the various floors really looked like.  First of all there was 2 different kinds of wood, hemlock and spruce.  We had ordered yellow pine. To add insult to injury we ordered a better grade of wood then was in place. So now what we have is the beautiful old floors , especially the hemlock in the hall, kitchen, my office and girls bedrooms with lot's of character and knots and the narrower and more yellow spruce in the living room, our bedroom and Bob's office also with knots and the pieced in places with yellow pine that is knot free!!!
Problem #2
As much as I wanted bleached, white stained floors it just wasn't going to work as you can see below!
 Plus I had a floor sanding guy who wasn't willing to try much of anything different.  After sampling various colors and products I decided to switch to a pale gray stain thinking that could make the woods blend better and still give a similar light, Nordic feel that I was looking for.  I found a stain by Rust Oleum in a light gray, tried it out in the living room ( spruce and yellow pine ) and after much discussion decided to go with it.
The middle color below was the winner.  If you look towards the center of the boards where it's put on thicker it looks like the boards sorta, almost match.
Problem #3
Apparently Lowes is the only store anywhere within a 100 mile radius that carries the stain BUT they were discontinuing it! The Lowes by me had only 1/2 pints.  After spending 2 hours at the store with a friendly paint guy we located the amount we needed ( all in quarts ) but in 6 different Lowes.  So drove she did ( or I did ) 30 miles in one direction and 60 + in another gathering quarts of stain.

Problem #4
Stain Day- I show up with my many quarts of stain the next morning, we start laying it down but this time on the hemlock section and ....... it looks like crap-ola!!  It was to orange-y- blue in real life and blotchy depending on the grain of each board.
End result -  we quickly switched gears stained the new boards a weak solution of Minwax Puritan Pine to even out the color and make it blend more with the old floors and put a clear poly everywhere. As we were moving in less then a week we really had no other choice.

Problem #5
Most of the floors look pretty good despite the fact that I really didn't want natural floors.
 The only place it really looks different is in the living room nook. The floor guy swears it's the same and it's just the light but no matter how I look at it, it just looks off.
So several possibilities: 1. it will darken and match over time, 2. we buy new rugs to cover.