There is no real easy way to do it properly without completely disassembling the looms. The ones I have done, Toyota seems to twist the wires around I would guess to keep things nice and tight and reduce any stress from pulling on one wire (so if its going to pull, it will pull on the whole bunch). And there may be joints along the way so if you try to pull it from one end, you could end up breaking the wire and that would be a bitch to try and trace back later on.
Best way I found to do it is to start from the plugs you want to remove and work your way to each end (I usually started from one end to the other). First you have to strip off all the tape and conduit and use masking tape to keep things together. That way its easy to keep the shape you want and then if you find other wires you need to strip, you can go back pretty easy. Then once its all done, start taping up the loom like factory.
If you dont know already, the first few pages of this file will help with working out how to depin the plugs so you dont have to cut and tape them. Just remember that the plugs in the engine bay all have waterproof grommets so if you remove a wire with a grommet, you need to replace it with a blank grommet (if you cant salvage it from another plug, the part number is in the file as well towards the back - so you can buy them from Toyota/Amayama).
Here are some pics I have from one of the looms I did, the biggest one too. While it doesn't show much, this was the main loom running across the firewall and weighed in at 9kg and I was able to take out 2kg of wiring and modules (last pic).
And done before taping up - you can see all the conduit has been put back in place loosely and the masking tape I used to keep things in place, branches in the right spots and mark up what plugs into where when it went back in.
This is what was removed, the hydro fan setup was kept complete and is on the right.
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