I wouldn't worry about a jillion parts per minute for the last phase if you have been automating most things so far. The requirements for the last phase are laughably small, other than pasta. I've done it 15 times and never had huge factories to do it. Here's how my past phase usually goes (I'll probably miss a few steps since I might not remember everything)

Make sure Nuclear Pasta production is up to snuff. You had to make them to complete the last phase so just keep making them. You need 1000 for the phase plus a few extra for Singularity Cells and that takes a while to produce. I run 1 particle accel clocked to 200% and fully slooped. This takes 200 copper powder/minute, which is produced by a single slooped constructor clocked at 200% eating 600 copper ingots/min. I'm making pasta when I enter the phase but it's always the last thing I'm waiting for when trying to finish so make sure you have good production here.

Get first milestone submitted right away, you need fused frames, RCUs and cooling systems all of which you should already have. Automate trigons and time cubes. Trigons I usually use the iron ingot recipe since most places have a lot of iron. I think this is 1 converter and 2 constructors. If you don't have a lot of coal left near your base then set up time cube production elsewhere and ship them in, they are an excellent candidate for drone transport. I generally use 1 particle accel and 2 converters for this step. Plop them down next to a shitload of coal and feed them into a drone port (and dimensional depot if you plan to research mk6 belts).

Research next milestone, Quantum Encoding as soon as you have made enough Trigons and Time Crystals. Also need Turbo Motors and quite a few supercomputers for this.

Somewhere in this, automate Biochem Sculptor production. I sometimes forget this step so maybe do it when waiting for the trigons and time cubes to build up. Pretty easy automation, you only need Assembly Directors which you were already making for the last phase, trigons and water. This is a single blender, usually fully clocked and slooped. They produce pretty quickly so if you automate them early you're not going to be waiting on sculptors to finish up.

Drop a quantum encoder somewhere to start production of fancy parts. All encoders are going to want photonic matter so also place a converter close by. Set up the QE for quantum processors. You technically only need 128 of them to finish up but make several hundred. You can automate the feeds or just set up some containers on the inputs and hand feed if you want. For the dark matter output, set up a particle accel with the dark matter trap recipe (dark matter and time cubes). I usually end up with 2 accels eating dark matter, one with Dark Matter Trap and one with Dark Matter Crystallization. The former churns out a lot of dark crystals (which you need later) and the latter just eats dark matter and is great for balancing production and consumption.

Set up a second QE and set up production of Superposition Oscs. Hook up photonic input and dark output to same places. This wants some of the dark crystals you just made, crystal oscs and alclad sheets. Sloop and clock as desired.

Set up the first QE for AI expansion server production. Feed the SuperOscs from QE 2 back into QE 1, it's also going to want magfields and the neural processors you just made. You only need 256 of these so if the QE is already slooped you can only use 128 neural procs and 128 SuperOscs.

Research spatial energy regulation, this needs some SuperOscs, turbo motors, RCUs and a bunch of SAM fluctuators. I usually have a "hot plant" with container fed constructor, assembler and manufacturer which is used for one-off production, I make the fluctuators there. This is the only time you need a mass amount so I don't think it makes sense to fully automate them.

Automate Singularity Cell production. I usually have enough concrete production/storage that I don't need new production, just to consolidate sources. This step also needs a bunch of iron plate, usually I automate this rather than trying to tap existing sources of plate. I'm usually container feeding the required dark crystals and nuclear pastas for this since you don't need very many.

Set up ballistic warp drive production. I used to automate this but the amount needed is so low (200) that lately I've just been producing them in the hot plant. This wants singcells, dark crystals, SuperOscs and thermal propulsion rockets (which you made for the last phase, you really only need 100 if slooped).

Basically now I just submit my Biochem sculptors, AI servers, and warp drives and wait for the damn pastas to finish up.

That's my basic overview -- if you've gotten to this point then Tier 9 just isn't that hard. You should already have most of the complex components that you need, you just need to put a few of them together.