I actually just wound up sending my ships the long way around because I wanted to get the mission over with (my economy was a mess), but to address your points:
You can send your troops with mining modules through the iconian space. Once they are through, upgrade them to transports.
I assume you mean colony modules here, as they're the only other kind that allows you to carry population.
You will have less invading troops so if you have spies, use them to both reduce the morale of the Yor and their population by placing the spies on the spark improvement.
Because of various bugs and other difficulties (Dread Lords are much harder to fight under the new combat system, which means missions like Apocalypse where it's an all-out war against them are nightmarish) I am playing the game on the original Dread Lords, not an expansion, so this is out.
Another option is to create a custom made troop transport using adv. troop modules and a lot of engines. If your speed is around 8 or 9 you may zip right through iconian space without them declaring war on you.
Unfortunately, when I tried the Iconians declared war anyway. It seems like they don't want transports anywhere near their planets.
You can also try purchasing the troop modules from the Iconian themselves.
I tried; they refused. I didn't have a lot to offer as they out-teched me badly. The entire mission was basically sitting on the sidelines as the Iconians and Yor slugged it out.