E-Commerce Consultant and Designer that has created over 300 e-commerce sites ranging from small business to billion dollar companies.
Not at all. If you stick to white hat methods that have always worked great, updates will never hurt you or change your methods.
It depends a lot of in the skill sets and experience of both people but in most cases the ux designer should be controlling the developer pretty heavily in order to make sure his ideas come through properly.
The UX designer may just need to work on his approach so people don't feel bossed around and more like they are working together.
In an ideal world, there would be a project manager who makes sure everything is communicated well and keeps the dynamic feeling great.
From the looks of it, you might have to hire a PHP developer from Elance or ODesk to write something custom. There are tools that can find the results but its going to hard for them to remove certain ones automatically.