Is there a way to rebuild just gdb, or at least some fairly small
  subset (including gdb) of the tools?

symlink /usr/obj/auto-3/tools/bin/nbmake-sparc to your bin dir, and then
you can just go build gdb (example for netbsd-4 and i386):

gdt 66 ~/NetBSD-4/src/gnu/usr.bin/gdb6 > /usr/obj/gdt-4/tools/bin/nbmake-i386 
all ===> bfd
all ===> libiberty
all ===> opcodes
all ===> libgdb
all ===> readline
all ===> sim
all ===> gdb
all ===> gdbtui


Then you can install to destdir and to the real dir.  Note that I'm
doing UNPRIVed builds; you can install the etcmanage package and read
BUILD-NetBSD that i use.

fnord gdt 68 ~/NetBSD-4/src/gnu/usr.bin/gdb6 > nbmake-i386 install
install ===> bfd
install ===> libiberty
install ===> opcodes
install ===> libgdb
install ===> readline
install ===> sim
install ===> gdb
install ===> gdbtui
fnord gdt 69 ~/NetBSD-4/src/gnu/usr.bin/gdb6 > sudo nbmake-i386 DESTDIR=/ install
Password:
install ===> bfd
install ===> libiberty
install ===> opcodes
install ===> libgdb
install ===> readline
install ===> sim
install ===> gdb
#   install  //usr/bin/gdb
/usr/obj/gdt-4/tools/bin/i386--netbsdelf-install -U -M //METALOG -D / -h sha1 -N /n0/gdt/NetBSD-4/src/etc -c -p -r -o root -g wheel -m 555   gdb //usr/bin/gdb
install ===> gdbtui
#   install  //usr/bin/gdbtui
/usr/obj/gdt-4/tools/bin/i386--netbsdelf-install -U -M //METALOG -D / -h sha1 -N /n0/gdt/NetBSD-4/src/etc -c -p -r -o root -g wheel -m 555   gdbtui //usr/bin/gdbtui


Beware that if you are debugging libs that gdb uses, you'll have to do
that to, but you should be able to whip up a script to build those and
gdb and do the installs. That should cut things down to well under 30
minutes on your SS2 :-)