I've been using 4.0.92h on an intermittently connected 486 for about a
month. The new "burst mode" is specifically intended for such cases,
and it seems to work pretty good.

There are no incompatabilites with the in-tree version to speak of:
the daemon is called "ntpd", not "xntpd", it's built static, and if
you inadvertently call up the in-tree ntpq or ntpdc against a version 4
daemon there's no harm done, you just have fewer capabilities.

I supplied a patch to build the Sun IRIG driver, but it really should
be tested by someone with an IRIG connected to a /dev/audio device.