I thought Lexus uses Nakamichi unit?
It’s unfortunately that some places can’t be bothered or they just don’t know anything about the product they sell to answer your questions. You really need to find a place just encase you need extra help or for other stuff. I haven’t done car audio installation in a while so I’m a little behind with newer vehicles.
For power you need to get the power from the battery.
Red (+) goes to the positive power for the Amp. Put a fuse near the battery terminal. In any event the wire you run shorted with the chassis, because we don't want your car caught on fire.
Black (-) can be taken from the chassis of your vehicle, find any bolts screw on your chassis close to where the amp is going to be located and connect it to the negative part of the amp.
Yellow (acc) need to be connected to Accessories, usually the wire that’ll turn your car audio on when ACC from the ignition switch is selected. Underneath the dashboard is the best place to connect this wire if you don’t want to open up your car stereo. You can check the ML Sub amp because you might be able to take it from there too if the wire is not like the DIN connector wirings. I prefer to make my own switch if it’s mine but you need to turn it on and off manually.
My suggestions of two speakers were for your 16 Ohms amp. So you don’t need to install two subs anymore if you add extra amp. You can install two speakers if preferred but use 8 ohms connected in parallel or 4 ohms in parallel then switch your amp to 2 ohms, or just get 1 bigger speaker at 4 ohms. Another is to use stereo amp and connect two lower power speakers on each channel which is better than 2 speakers in parallel.
One thing I recommend is that don’t remove the old sub because it need to support the others speakers to fill the frequency gap that the others can’t produce.
Are you going make your own enclosure or get a pre-made box?
http/www.alpine-usa.com/US-en/products/product.php?model=MRP-M500&lang=en&tab=F you need 10A on this unit so get a wire guage 14AWG max load for the wire is 20Amp but start with 10Amp fuse and if the fuse blow up then increases by 2 = 12Amp until it stop blowing up.
http/www.alpine-usa.com/US-en/products/product.php?model=SWE-1043&lang=en&tab=F
http/www.alpine-usa.com/US-en/products/product.php?model=SWS-1023D&lang=en&tab=F
http/www.alpine-usa.com/US-en/products/product.php?model=SWE-1243&lang=en&tab=F
Among the three speakers I prefer the SWS-1023D but they’re all good whichever one of those you chose. One of these units is more than enough for your vehicle. If you need more power then you need to upgrade you electrical distribution. As for wires for these speakers you need to ask the dealer whats best suite it needs. standard speaker wires are fine so you don't need to get fancy on it.
Sorry if my explanations aren't clear then let know.