When I stored a few bikes for 3+ years while we went OS, I did the following to each:
1) Completely drained & empty the tank, then suspended a Silica Gel sachet on a string in 'mid-air' within the tank, closing the cap on the tail of the string.
2) Changed the engine oil
3) Place bungs in the airbox inlets and exhaust outlets.
4) Get all tyres (there was an outfit among the bikes I stored) off the ground using appropriate combinations of centre stands, blocks, whatever.
5) Remove all the batteries so my Dad could cycle them through the battery charger every couple of months.
6) Put a bike cover over each one
They were all stored in a 3x3 colourbond shed, so not too different to a shipping container.
For the record, all the batteries, regardless of their age when we left, lasted a little over two years before they stopped accepting charge, so I was up for all new batteries when I got home anyway.
My wife's Ducati was the first to awake. It received a new battery, a tankful of fresh fuel and after a reasonable amount of cranking (due to the vacuum fuel shut-off with no 'prime') fired up happily.
The XS11 outfit was next. It fired up fine with a new battery and a full tank, but then proceeded to leak / weep from the petcocks for a while,. This was fixed by a combination of the old shrunken seals expanding after being in contact with fuel for a while and me stripping and re-assembling the petcocks. I stripped them to see if anything obvious was wrong, came to the conclusion I needed new seal kits, put them back together and then they stopped leaking before I ordered the parts. That was three years ago and they are still fine.
Similar stories with the other two bikes as well. The only real 'casualty' was the front brake master cylinder and tank finish on the XS11. I left the bars on full right lock and the bore seal on the brake master cylinder failed, letting the fluid weep out and drip onto the tank over the course of the three years. My XS11 now sports a master cylinder from an FJ11. The paint damage is still there. Neither the original master cylinder or tank were in the great condition before storage, so no huge loss on either accounnt, though the bubbled paint still annoys me to look at.
I had originally planned another step, which was to remove each plug and squirt a little Inox into each chamber. Might be worth considering, but I didn't do it in the end.
As far as rego goes, I think the best you can do is make sure you retain your final rego papers and other documents that prove ownership. If other states are like NSW, once you let your rego run out over an extended period, you have to start from scratch as if you've just bought an unregistered vehicle from someone else's shed - buy new plates, the lot. I knew this when I decided to store them. The savings in not paying rego & insurance for three years easily covered all the once-off costs of re-registering them, though I occasionally have flash backs and quote the wrong rego numbers... ;-)
PS: None of the bikes I stored were watercooled, but if they had been, I'd have taken the same approach to that as I did with the engine oil - change it for fresh stuff before placing the machine in storage.
