I've seen a nicely manufactured [&] 486 that has 4 PCI, 1 VLB, 3 ISA
   with Intel chipset.

This sounds like the ASUS/AUStek PCI/I-486 SP3G.  I've been hearing a
lot of good things about these boards, though I haven't used one
myself.

   - does netbsd work well with the NCR PCI scsi?

It worked well for me last time I used it (on an Intel Pentium box).
It works for other people.

     I currently have
     an AHA 1542CF which I know is the bottleneck (my DEC RZ26 disk
     is definately faster than the 1400K/s I currently get)

Or the file system parameters are abysmal.

   - I assume that the PCI scsi does NOT have the 16MB limitations
     that the AHA1542 has? 

No, it does not.

   PS: Cost is AU$215 for M/B, and AU$110 for card, [...]

Does that include the CPU and/or memory?