Generally I would want more knowledge, I would say. Having Mark III/IV cruisers and bombers will make such an enormous difference for you, but that's 10k knowledge right there, I think. Adding some upgraded zenith bombers could also make your assaults a lot easier, but they are pricey to use, to sit depends on what you want to do. Raptors and tanks might be good in a support role, too. Out of that mix I would be tempted to downplay shuttles and bulletproof, but it depends on what the AI is using.
If you put 10-20 mark I science labs in a transport, take that transport to an enemy planet, and then send it way out into the middle of nowhere and eject the science labs, you can do flash raids for knowledge on enemy territory with great ease, really. I am really surprised that you don't have more offensive tech unlocked by being at that AI Progress -- you might want to do some data center raids, too. To take the final planets, I feel like you're going to need more offensively, but with flash knowledge raiding it's not like that will take forever to prepare for, and you should be able to do that without increasing AIP much or at all further.
Others might recommend other various starship upgrades (MkIII raids was a good choice for your purposes now, I'd say, though), but I tend to be more of a fleet ships kind of guy. You'll just want to be sure and kill those orbital mass drivers before you bring in your starships to planets that have them (like probably the final planets).
You know, I said ignore the bulletproof fighters, but if the AIs are favoring bombers heavily, then you might want to invest in your various fighter lines a lot, in general. The zenith bombers are what will help you make shorter work of their fortresses and core forcefields (as well as the home command stations themselves), and thus overall shortening your engagement on those planets, which is why I was suggesting those.
I would suggest using transports to dump bombers right next to the mass drivers that you want to take out. That way your ships are not alerting the enemy until the last second before they strike, and then if you either scrap those bombers or put them back into the transport to retreat them, the AI won't stay on alert. They won't stay on alert unless you kill the planet next to them, so you can use that to your advantage. Do a blitz against them, destroy something that is in your way, and then get the heck out. They'll be a bit stronger in other areas there from reinforcing, but you'll be one step closer. Then when the things like the orbital mass drivers are all gone, you can make sure you come back in with overwhelming force and hopefully take them all in one go, or close. Normally that is not easy to do, but with your combination of pretty powerful secondary ships, if you can muster the energy you have a shot at it, I'd say.
For the guard planet, if you nuke it that will alert the AI homeworld -- very very bad, unless you are poised to kill the home planet. Better to use transports, or even just to carve a path through the guard planet and just ferry your guys manually (back when transports were too brittle to be useful on core planets, that is what I always used to do -- worked well even then). Your focus on the guard planet is to make a path through it to the home planet -- doing whatever that entails -- and then otherwise to probably leave it alone. The longer you fight there, with tons of guys, the more likely you are also alerting the adjacent home planet.
Good luck! I actually think it sounds like you are in a potentially really strong situation if you play your cards right.
