The cooling system should be no trouble. As long as the block sensors can be swapped, you should be fine (I've not checked.)
Check your 90 for a knock sensor, down on the driver's side of the block near the oil pan rail. If it's not there, there's no trouble. If it is there, you might want to drill and tap a hole for it in the new block - the boss should be there, just unmachined.
You can use the 90 head on top of the 00 block without any trouble, and re-use your top end parts (it will save you work,) or you can go to the trouble to use the 00 head - the injectors and most of the top end sensors should hook right up, but the TPS will have to be adapted, and I think the MAP sensor is different - again, I've not checked (it's on my list.)
The final result is up to you - but we're here if you have questions.
5-90