I got a conversion kit when I done mine and it was a pretty painless exercise apart from a few hiccups which you will know to avoid after I tell you. Mine only took a weekend and I done it on axle stands on my driveway.
Watch out for conversion kits which come from a jzx90. Although they mostly work, you will need to change a few things:
jzx90 manual brake pedal wont work unless you also have the jzx90 booster, the brake pedal ends up way too high. The way around this is to use jzx100 booster and cut down the automatic brake pedal, which I have done on mine.
The front half of a jzx90 drive shaft will need the hanger bearing swapped over from your jzx100 auto drive shaft as it is too wide to fit in the jzx100 tunnel/mounts.
jzx90 clutch line is almost right, fairly easy to reshape a few bends though.
Obviously you wont have these issues if you get a jzx100 conversion kit.
Eitherway, you will need to cut a nice section of your tunnel out (forward of the existing hole) for the remote shift section of the gearbox and make a new box/tunnel to sit on top over it. OR get jzx100 manual tunnel section.
I didnt hook up any speed sensors on my r154 as they had different connections from my loom (loom was 2 wire, sensor on r154 3 wire) speedo still works off the abs sensors on all 4 wheels, am told that abs might not function correctly without a pickup off the box though.
Starting the car is as easy joining two wires on the automatic gearbox loom. reverse lights are the same.
Also if using a 2nd hand clutch and its pull type, you don't actually attach the pressure plate to the flywheel until you have bolted the box onto the engine. You sit the clutch on the input shaft on the box and then tighten bolts through the inspection covers. (i only realised this once i was under car trying to lift box up over the clutch
)
4age flywheel bolts are interchangeable for 1jz, should be easier to find.