The 1JZGTE swap isnt that difficult in the SC300, be somewhat a littler harder in the 400 and time consuming. The wiring is extensive and tedious but doable. Just dont do all the wiring conncectors in one spot, do it about 1-2 inches apart for each plug. Getting power to the ignitor, coils, and injectors, was a task, but also can be done in the wiring. I chose to run seperate relays just for my piece of mind. You can the stock SC300 ac lines, fan, fan shroud, radiator, power steering resevoir, motor mounts( some choose to use the more supportive TT mounts, Shorter), brackets, use TT upper and radiator hoses, the 400 you can remove the tranny mount cooler in the front of the engine or opt to leave it and use it if staying with the auto tranny. You can run 3" piping under the passenger side headlight, but you have to grind or break off a plastic tab under the light. It affects it in no shape or form of the light leaking. I chose to use the 94 Camry throttle cable, a little long, but works. You can also use the stock one, but the black tab on the cable needs to be grinded off a little due to the stretch fit. You can also use the stock 400 cable for the cruise, but it has to go across the valve covers, and looks tacky in my book. If you choose to run a AEM V2 standalone with patch harness, it doesnt come prewired for the AC to work. You can tap into A17 and A27 and so on for it to work as normal. There is more stuff, this off the top of my head.
If converting to a manual the lines in the firewall are there for the drilling of the clutch master cylinder. Just pull back the black insulation. You can use the MKIII or stock SC300 or the MKIV cylinder. the MKIII requires mods and also the pedals do to for the correct fitment in the foot well. The SC300 stock ones are best. The R154 or W58 is also doable and even the V160, yet expensive and getting harder to find. You can also use the stock 400 tranny bracket for the support of the three tranny. i chose to weld the factory holes and drill where needed. Sometimes the tranny doesnt come with the mount If you choose to run R154, you have to extend the shifter 4" back to fit correclty in the console area without further cutting. This is only deemed if you get an MKIII tranny and not a true Soarer that has the true extension already on it. Now would be a good time to replace the front and rear seals in the MKIII, replace the seals and bushing with MC, and vent the top housing plate if not using the Soarer. Presure builds up in the tranny and it must go somewhere. You can use the front half of the MKIII drive and the rear portion of the SC00 automatic. Check the center bearing and rear bushing for cracks or worn.