Looks like you have a pretty good list of the bits you need.
Clutch:
Make sure you do the thrust bearing with the clutch some kits may not include it but most will. It also might be a good idea to replace the thrust bearing retaining springs as yours will most likely be rusty from the few submersions you have had over the years, this goes for the clutch fork retaining spring as well.
As for the clutch fork, I am very sceptical that it is the cause of the juddering. The fly wheel is held central by the engine, the clutch plate is held central by the gearbox, the thrust bearing should by design centralise itself on the pressure plate and the clutch fork is pivoted on its mount and at the slave cylinder meaning and potential minor bends should be compensated for. By all means if it looks bent or damaged in any way (rusty, cracked etc) then replace it but otherwise my opinion is that it would be a waste of money.
More likely the judder is caused by damaged clutch plate or pressure plate or flywheel surface.
Clutch alignment tool is nice but can be done without it, just a bit of a pain getting everything lined up again.
Now I have written all this about clutches I have just had a thought... Your box is a 4 bolt, no idea if your clutch is the same layout as mine...
Timing belt and water pump:
Good idea to replace. I would be inclined to replace the tensioner whilst its out. Even if the tensioning device seems to be in good condition the pulley on it will not be provided in your timing belt kit and if you are unlucky that bearing may be on the way out, especially with the age of the engine. If the tensioner is good it should not be easy to replace and should not have rust or evidence of oil leakage around the piston in it.
Does your timing belt kit include cam seals and front crank seal? If not you should do these as well, much easier to do whilst the motor is out.
Valves:
Check your clearances whilst the engine is out, much easier to do than in the car.
Engine mounts:
May as well check they are in good nick whilst its out.
In terms of the difficulty of changing engines over i did an ej202-ej202 bare engine swap (new engine already prepared for install). Removal, swap all sensors and manifold over and re install back in car was easily done in a day. The swapping parts between engines was far easier than i was expecting, (12 bolts on the manifold, knock, crank sensors and temperature sensor plug, ecu and mounting and unplugging leads for the spark plugs the plugging them back on new motor and thats it) again not sure what differences there are on the ej20j/ej22 but i would imagine very similar.
Any my last tip is have some ratchet straps handy, sounds strange but I 100% sware by them. I discovered that when pulling/installing gearboxes/engines that can be used to pull the box an engine in different ways small amount to get them apart/back together/line up better than anything else I have tried They can support weight, pull, push, change angles of heavy components etc. I will never ever pull a gearbox again without them.
If I think of anything else of use I will add it
