1. If this is a one-off thing, then you get an ISBN. IINM, the allocating authority in Malaysia is the Malaysian National Library (Perpustakaan Negara Malaysia). It's free! Details here. http://www.pnm.gov.my/index.php?id=235

2. If it's a periodical (published every month/week/etc), then you'll want an ISSN. Details here. http://www.pnm.gov.my/index.php?id=237

3. Where to keep the books. Don't worry.

If your book is 5mm thick, 1000 of them would measure 5m when stacked up. If you limit your stack to 1.5m (so that it does not topple over), your 1000 copy print run will fit on 3.5 stacks. Not a lot of space. Even if you've got a really thick comic, and each is 10mm thick, 1000 copies would still fit in 7 stacks.