If the Honda engine is larger, you are completely hosed. If it turns out that it rotates in the opposite direction, I wouldn't be willing to take on that challenge either. I have the 1.3L 5MT in my Suzuki Swift (a 1994). It is pretty tight when you are trying to do anything that requires work on the passenger's side of the engine (alternator, timing belt, etc). I had to cut off the extra auxiliary pulley to change my timing belt earlier this year (believe me, not what I had in mind), and working on the alternator wound up being tight quarters too. I figured that if at some point I need to swap the engine, I would do so for an xfi engine (if one can be had) or for a 3 cylinder anyhow. It would just be so much easier to work on things, and my MPG would probably go up also
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