I am sorry things are not looking on the up and up for your new kitchen. :( After closely inspecting your photos and the plans, I did noticed a couple of things. The base cabinet is not centered under the window to begin with! Look at the plan, not the drawing of what the kitchen should look like. Looks to me that the window is in the correct place, but whoever designed the cabinet layout has placed the base cabinet off center of the window. That would bother me big time! (I have a similar issue in my 10 year old kitchen. I pointed out a minor misalignment of the cabinets to the cabinet designer after my cabinets were hung, and she just shrugged. I wish I had noticed it on the plans. The thing is, it would have been an easy fix, and still is, if I had insisted. I let it go and I hardly notice them now. Also on your plans... instead of a wall, there is suppose to be a refrigerator cabinet surrounding the fridge. Not a wall on the one side. However, I agree that extending the wall would be an easy fix. As for the base cabinets on either side of the range, the one nearest the door looks to be a 12" or less base, where the plans say 18". Granted, there is not enough room for an 18' to begin with, but there is for a 15" base (if that is indeed a 12" base in place.) I believe that the base on the other side was suppose to be a filler, and not the 12" or less that they have in place. Not sure what happened there! If I were you, I would get the person who drew up the plans involved. Don't back down until you are happy. Best of luck!

Your money, your home you are not being to picky. So how I dealt with this during our house renovation when things looked rough I simply asked my husband or the guys doing the work if they would accept this quality of work on their ( insert here car of their dreams). For my husband it was if this was your 57 corvette would you accept this, he would take a deep breath think about it and assist me getting the quality we were paying for. I do understand perfection has limits, but know that a decent finish is possible even merging old and new walls. Be polite, be firm and get what you are paying for.

At this point, the job ($4/sf for a BIG job with LOTS of things to do = awesome price) is finished. The cure is going to be worse than the disease. I'm a big fan of "Wait until you have a problem before throwing money/time at it." It is the cheapest solution I know of (I'm a pragmatist...who is both cheap AND lazy ;-P). My advice is this: leave it alone. Keep 10% 'extra' of the flooring product (roughly 75sf or to the nearest box). This will offer you the peace of mind and the material security you will need to feel secure. You will keep it in the back of your mind. You will know that IF something goes wrong you have ALL THE PRODUCT needed to repair/replace the damaged planks. With a laminate floor I wouldn't worry to much about a bit of bounce. People have 'put up with' bouncing laminate floors for 20 years (the SAME laminate they installed 20 years prior). That tells me the click system is fine. Your floor is a rigid vinyl (8mm thick = nice product). The rigidity of the core will help keep everything stable. The only weak point (as in everything in life) is the link (click edge) between one plank and another. This is the one and only place things *might go wrong. Now to be blunt, a rigid vinyl floor like yours can be taken apart and, "in theory", be clicked back together - BUT I don't like that idea. I really don't. We know the click-edge is delicate. We know that. We've seen them brake by grazing the ground before being installed. A vinyl floor that has been disassembled has a STRONG likelihood of DAMAGED edges. If the edge is damaged then there is almost no way you will get them back together. That means you will have to assume 25% damage should you choose to 'unzip' this floor to the point where it bounces. That leaves you with 75% intact flooring with 25% garbage planks (which must be replaced). As soon as you try to fix the subfloor underneath (by removing the flooring) you will have lost the 'intact' floor. You are guaranteed to spend MORE time, MORE money and MORE materials to deal with this. Compare that to 'leave it alone'. Right now you have 100% intact flooring. Every day you wake up to 100% intact floor is another day with a perfectly functional floor. Every day you have 100% intact floor is another day you have SAVED time, money and materials. Simply leave this floor alone until something MAKES you repair it. Keep your 5%-10% extra on hand for future repairs (and there will be future repairs). Use them if and when you need them.

Tough to tell from 4" away but it does not look great this far. Who is doing the the tile install? Did he do the waterproofing? The pan? The floor test? Any pics from before he started laying tile? My concern is it looks like he is using a tuning system but still has some severe lippage, and typically when the surface does not look good the hidden stuff does not get better.