I got 2.4.21-pre4 which has your x86_64 updates. It works MUCH better.
Still some problems remain:
1. One unknown ioctl is logged from RH8.0 init:
ioctl32(iwconfig:185): Unknown cmd fd(3) cmd(00008b01){00} arg(ffffda90) on socket:[389]
2. gdb still seems broken. gdb ./sleep [where ./sleep is simply main() calling
   nanosleep(), but linked with -lpthread] hangs or loops and takes forever
   to respond to ^C.
3. bootsect.S still needs a patch to prevent 'bzdisk' kernels from
   disabling the FDC
/Mikael
--- linux-2.4.21-pre4/arch/x86_64/boot/bootsect.S.~1~	2002-11-30 17:12:24.000000000 +0100
+++ linux-2.4.21-pre4/arch/x86_64/boot/bootsect.S	2003-01-29 16:08:38.000000000 +0100
@@ -395,9 +395,15 @@
 # NOTE: Doesn't save %ax or %dx; do it yourself if you need to.
 
 kill_motor:
+#if 1
+	xorw	%ax, %ax		# reset FDC
+	xorb	%dl, %dl
+	int	$0x13
+#else
 	movw	$0x3f2, %dx
 	xorb	%al, %al
 	outb	%al, %dx
+#endif
 	ret
 
 sectors:	.word 0
-
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