I think you are exaggerating the losses. 2k financially a year sn ba felt, but it is not the end of the world if you are already on a decent salary. Certainly not enough to not take a potentially good job for.
Its relative to salary and as it hasn't been mentioned what the OP's salary currently is, it would not be fair to comment on it being anything other than a factual figure. £2k net is still £166 from your take home. Even to someone on £26k per year that's the equivalent to 10%. A 10% pay drop is still relevant.
I am making an assumption that it isn't a hugely paying job as otherwise I would expect the OP to be offered at least the same as he was now. No reason for an employer to offer someone £39,300 if the candidate is what they are looking for and currently on £40k, however it is more relevant if the candidate is on £20k currently and the only have budget for £19k and have already stretched to £19,300.
As for untold value in the loss of commute time... not it is not "untold value", it is a 25 minute drive. His previous situation of 10 minutes walk was the perfect, idyllic scenario as far as commutes go, and almost any switch in job is going to change that. Certainly not enough to not take a potentially good job for.
Untold value is a fair comment. I don't know how much the OP values his own time. Does that 30 minutes extra travel time affect him seeing his child/children in the morning, or will it stop the OP seeing them at night before bed, who knows. Is that 30 minutes of extra travel time a conservative estimate at best and could it be considerably more at rush hour times thus being 1hr per day extra travel time. I don't know, so yes I cannot put a value on it, and neither can you, that is for the OP to decide.
I personally value my time quite highly. The extra travel time to me personally would mean not seeing my daughter in the mornings, or when she was younger it would be at both ends of the day, and you cant claim that time back. Once your kids grow up there is no going back and it makes a difference.
So to me, a pay cut and extra time out of the home is a double blow.
Loss of holidays is a shame, but if he was already on 28, which is higher than average, then going down to a regular 25 is also not the end of the world. Certainly not enough to not take a potentially good job for.
The OP has dropped 8 days of holiday in total. He had 28 + bank holidays, he now has 20 + 8 bank holidays. 8 days is 1.5 weeks of work equivalent, again not to be sniffed at.
I accept he will take some hits, but if it a choice of stay in a dead-end job that he hates, and going for a new job that can lead to a better career, then for anyone with ambition the choice is definitely appealing.
There's nothing wrong with taking hits, but there is also nothing wrong with not jumping at the first chance you get and assessing your options more fully.
No short sightedness, no over exaggerations. Just balanced thoughts for the OP to consider.
As more information is coming to light from the OP its sounding less like such a terrible choice, but its still not a slam dunk.