How to avoid disrupting the narrative in a scientific paper when you have done too much work
My field is biomedical so comments may or may not work for you. In our works, sometimes protocols did change along the way and occasionally I need to explain that in the paper. Hopefully these comments are general enough to be useful to you.

The primary goal is to think from the gain of the reader and maximize the gain:pain ratio. You want the ratio to be high: transferring the most to them with them going through the least amount of effort to understand your work. With that reason in mind, here are some suggestions:


Really, very few people reading scientific journals are interested in the step by step saga in how we reach there. I know it may come off harsh but what matters to the researchers during the development process can be drastically different from what matters to the readers. So, cast a critical look and weed out details that are not bringing any gain.
Minimize the "we wanted to do this, but then we ended up with that..." frequency. Try not to start every single sentence with this kind of structure because they sound trivial and never-ending. Instead, I'd suggest setting up a section called "original plan" (to hint that something was changed) and give it a good introduction. Then, you can have a section called "Modifications" to briefly but sufficiently explain major design changes.
One device I found very effective is a graphical schematic. You can consider a graph of the original scheme. Then in the Modification section, use the first graph as blueprint, slightly grey out the contents, and then insert modified components in 100% black. Consider indexing the changes on the graph, and then in the text you can simply explain them sequentially.