You know I kind of forgot that you hadn't done this quest...😅 This was one of my favorite ones... I have several now that I've had a chance to pretty much see how the entire game plays out.
You couldn't get the landing gear that fits under your ship because that vendor doesn't sell those. I usually put a landing pad with ship builder on my outposts so I have a better selection of ship parts. I -think- it set up so anything you've ever bought will be available at your outpost. I can't really remember any more because I have a mod that makes ALL parts available. I got tired of running from vendor to vendor looking for the parts I want. The reason you couldn't add that extra engine that you wanted wasn't because of your reactor being too small. It was because you only had two bars left in the stack where it shows your engine power and that engine needed three bars.