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Retirement tax questions

I switched employers in 2018 and, due to a calculation error on my end, over-funded my 401k. My plan sponsor's deadline to provide an excess contribution distribution was March 1st and says I am too late to go through that process. 

It is clear that I will be double-taxed (it's too bad, but fine) and I will keep pushing my plan sponsor to see if they can make an exception for me, but I am having trouble understanding how I need to fill out my 2018 tax return, assuming I CAN'T get the distribution and amended W-2 before 4/15/18. 

I'm guessing the step is something like going back to my W-2 information and reclassifying my income so that less of it is tax-free and I don't exceed 18,500 in the 401k distribution box on my tax forms. Then do I also need to pursue a 1099-R in parallel to distribute the difference (which I will declare on my 2019 tax return). Is there something else i need to do? 

I am clear that I will be taxed twice, but am not sure how to do the proper accounting in 2018  and forms to fill out to make sure everything goes through appropriately... my plan sponsor is not being helpful.