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At this time it looks like an RB30 Skyline "stumpy" gearbox...
that should be MR30. The MR30 Aussie L24E Skyline and HR30 Japanese L20ET Skylines had the stumpy L series 5spds. The RB30 engined Aussie R31 Skylines have a long 5spd. Another note is to make sure you don't buy a Stanza 5spd (which is the same length) for this conversion as it has smaller internals and won't interchange like the Skyline box. Not up on all the gearbox codes, but the stanza 5spd has a dogleg 1st with reverse where 1st normally is so it's easy to pick the difference.
for what it is worth, for the L series and stumpy 5spd in my 1200 coupe, I only had to elongate the shifter hole a couple of inches. And I mounted the engine as far back as possible. I think 1000 4spd is same length as the 1200 box, so your shifter location would probably require a similar mod.
1000 trans tunnel is pretty damn small though. Keeping the original shifter position might be the least of your problems in that area. Do you have a manual or auto floorpan?