I am a bit confused about the differences and relationship between all these "wood fence", "make-shift fence", "temp fance", "retaining wall that's 1m into your land" you mentioned. It might help if you can draw a simple diagram...
If it's just the temp fence that Mrs G is not happy with, have a chat with your CSR/builder and mention about the neighbour's complaint, they will fix it for you quite quickly.
Trust me, before final hand over, your builder is even more afraid about any possible trouble from the neighbours than you. Imagine someone damaged the window or door or anything during this period, who's problem is that? The builder!
Make sure you take before and after photos this time. In case you need to take this matter further, this is something that can at least prove that you have done something good...
About the wall that should be removed, insist on it to be removed. If you see your neighbour's landscaper again or know his company name, get his contact details and contact him directly. Should be easier to get it done through him than your not-so-friendly neighbour...
May be you missed it last time, but it's never too late as long as you start taking photos. Digital photos are basically free and I took average of 50+ photos almost daily before, during and after the construction process. You might need some to support you against your builder or someone else some day, you never know...
Good luck!