Absolutely no way you got a real harness for a 1993 ES 300. No one has ever made any.... You can't... All OEM wiring goes from the HU, to the AMP, then is distributed to the speakers.
The gen1 300's have their amp under the passengers's seat. You can throw it away, bridge the correct input/output wires together and re-use them. But it is NOT a good way to do it. (The wires with the splices, make the quality poor at the best

, not to mention if you're pushing real power through them, they can't take it. They're designed for 20w peak loads, not 50w-100w RMS)
You need to rip-out whatever you got jinxed into buying, and install brand new wires at the very least, to the front speakers.
Now to your question... Four pair of wires. The door & tweeter speakers run off two pair, while the 3" (2.75") dash speakers run off two pair.
You can figure out what is what buy playing music and testing the wires, hitting a 9v to the wire pairs (listen to what pops) I like music better...
If you search ClubLexus.com's ES forum, you'll also find that all speaker wiring has been decoded into what speakers it is. (On both the HU location, and stock amp location. Wire color does change)
Also you're kind of on your own figuring out how the dual stage (tuned) antenna works. It's a three, or four wire system, and if you search ClubLexus.com's ES forum; you find that people normally wind up with their antennas looking stupid only going part way up.
Anyway... What I wound up doing was to throw all the crappy stock stuff away (speakers, HU, CD changer & amp) and hard wired my new HU in with new wiring. That's the only option to getting good quality, or higher power. You really need new wiring if you want both.