Cost plus means he presents you with the cost of the work, and then adds his % on top. Well problems are not foreseen, and need timely action to remedy. Most contracts have a time is of the essence clause, because things need to more forward. How much money are we talking about for the bills you are getting? 50K? 20% of the estimated total?

all in overages are around 60K. I've already paid about 30k of them and some of them I agree with but some of them seem extra. Like putting a couple shelves in a linen closet, things I would not imagine need to be specified or would have been considered an "extra".

Just to note I haven't received the estimate for the well yet that was just done, and I wish time was of the essence but it took nearly 3 months for the well to be moved. The entire project that was estimated at 12 months to account for supply chain/covid delays has now been more like 16 months and still not complete. For reference...house is about 2500sqft ranch/farm style

so not crazy big or complex.

In my experience too many contractors using a cost plus contract actually purchase and install items like they have a fixed cost contract.

To answer your questions as best I can. Generally speaking, a cost plus contract is all costs reasonable and necessary, so a contractor can't profit from his mistakes. But neither can you. Suppose you ask for an upgraded tile and the contractor never gets you the price of that upgrade but does the work and you agree it is nice. The contractor then presents you with a bill that is much higher than expected. You still have to pay for the upgraded tile as it is unreasonable to expect that you should have the upgraded tile for free, however, you might get the contractor's percentage removed as that is profiting from his mistake, especially if you argue that you would have made a different decision were you given the actual price.

This is the problem with overages that violate the specific terms of the contract. You still had the work done and should have reasonably expected to pay for additional work. However, items that should have been included in the original bid but were omitted are generally considered his mistake and shouldn't trigger an additional charge, but there is a lot of nuance to this because of unjust enrichment and damages. So it might be best to say... it depends.

Your contractor does have a reasonable right to keep the job moving forward by making decisions that would delay the project were they not made, but still must report to you in a timely manner. This is not really time is of the essence, but the verbiage doesn't really matter.

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So, if you plan to contest these costs then you need to see an attorney with experience in residential construction contracts. Really there is no plan B that is going to be as effective as a letter from an attorney. However, before you do that, look through the add-ons and see how many of them you would have authorized if you knew the cost prior to installation. You may well decide it is not worth your trouble.

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I really don't know enough about wells to answer your question on the proper procedure before drilling a well.

In my 50 year experience with Cost of the Work Plus a Fee construction contracts I believe it's essential that the Owners hire a professional to represent their interests.

We ended up 40%+ over on our cost plus contract. Basically we got hit with covid increases and my builder giving us a quote based on what things cost before covid and on the previous houses he had built just before ours, with owners that had lower quality/budget specifications. We discussed upfront that we would be choosing higher grade/quality/cost items, but he still underestimated and then covid supply/labor issues increased the cost difference even more. Your $60K was just one line item here, basically the quoted $60K for cabinets versus the actual $120K for cabinets. Once you get started with a build, there isn't much you can do but keep writing the checks!

Our build went well with our contractor so I don't have any input on how to hand him but we also had a well put in. With wells you just never know until you start putting it in. My husband and I crossed our fingers that'd it be under $20k. This was 5 years ago and we are (well we were at that time) in a lower cost of living area. Well had to go much lower than we anticipated and luckily the price was still under. The water isn't ideally what he well digger wanted to get into but it isn't dirty. Off the top of my head I'd be worried that it isn't deep enough. With droughts going on I googled what I should do, as a well owner. I didn't find anything about cutting back usage (that's a no brainer maybe??) but the main issue is individual wells aren't dug as low as other water systems and can run dry. What is your depth compared to others around you? If they don't know, or won't tell, I'd assume your county has the information. On our county website you can look at all the well permits (other water rights too) and depths.

60k sounds tiny to me but it depends on your total build budget. For us, like Chispa, drop in bucket. In our build we had a couple of overages that surprised us and weren’t clearly communicated. As a result we actually requested a meeting and clarified expectations moving forward. It did help. The thing with overages as the build progresses is that you may be able to adjust elsewhere if you know they are coming. But at the end, work is done. If the project is now completed you may want to end the relationship amicably. It’s also likely you will need the builder for deficiencies over the next year. So be careful how things conclude.