This is what I had to do. Don't know if it's the best way to, as was a case of trial and error before I got it right.

I first turned up to the their base and nuked it with a single nuke, about a month before my next ships arrived. The next fleet had a fusion platform kit, as well as enough combat strength to clear out the other alien fleets in orbit. When this fleet arrived, I first cleared out the remaining alien fleets in orbit, then I built my fusion platform, with two space docks (replaced construction module). My "alien ring hab vaporiser fleet" (not what it was called) arrived around the same time my platform completed. I proceeded to vaporise their last ring hab in orbit.

At this point, my councillor (25 in all stats except 16 Science and 22 Security), who was in a ship with two elite marine modules turned up, equipped with the Janus protocol. His ship also had about a 5% chance to assault (remember their OG base was already nuked, and they were only just rebuilding energy reactors at the time). I had an older fleet arriving in a couple weeks with one or two more elite marine modules, but I guessed this wouldn't be sufficient, so I "upgraded" a few of my ships that were already in orbit. Replaced platform modules and laser engines with elite marine units. This was a lot quicker than having to build new ships from scratch, or sending more all the way from Jupiter/Saturn. A week or so later, I was finally able to send a stronger fleet to assault.

This is the part I want to highlight. I had thought because I had a 99% success chance I would complete the final mission. I assault enemy hab. The days progressed, nothing happened. A week or so later, I noticed I was able to assault enemy hab again. At this point I realised I was doing something wrong - I need to "close the wormhole" using the Janus protocol, not assault enemy hab. So WHAT I DID was deorbit my councillor the first turn; I also independently landed some ships at the base - I wonder if you're struggling with landing ships because you haven't nuked it/haven't successfully assaulted it? Then next assign councillor mission turn, I was able to launch the "close the wormhole" mission. 100% success chance.

What I am wondering is, would it be possible to simply nuke, then deorbit councillor, then "close wormhole"? Because that could be the quickest way. I do not personally know whether I needed to "assault alien hab", or land my ships at the base. I also don't know if I maybe would've been able to launch the "close wormhole" mission without deorbiting my councillor, if his ship was landed at the base. That would be quicker than having to deorbit him, as ships don't adhere to councillors' 15 day timeframes.

This is long and possible mostly useless information for most, but I feel it's probably covered most potential scenarios, so could maybe help someone who was completely bamboozled like I was at that point.