In this universe FTL exists but arrival times can be unpredictable to say the least.
So a mechanism for this could be chaotically fluctuating macroscale worm-holes - ie, like a vibrating string, but of arbitrary length - so that gives you your variation in arrival date. Being worm-holes means that the physical distance is not necessarily a limiting factor, however - rather one needs to find (or navigate) a shorter path through the underlying structure of the universe (of which this is a 'hologrammatic projection into 4-space', if you will).
The advantage of that is then you don't need to give up so heavily on causality and other FTL problems. The disadvantage is that it's still 'magic'. A great example of a novel that uses a similar (but non-fluctuating) approach is Miéville's "Embassytown". This gives you an 'olde worlde exploration' feel (using space as a metaphor for the sea) to travel - with ships sometimes getting lost.
Alternatively, (if you are looking for roughly 12-months distances between 'ports') you could actually set the universe into a non-FTL that is towards the centre of a Pop III globular cluster - so that distances are shorter, and then you don't need to abandon relativity at all. This would allow for a 'new world' oceanic feel, great skies, and no huge plot-holes concerning causality, radio, time-travel, etc.. You would still need an inertialess drive in order to accelerate/decelerate fast enough. Maybe there's a side-effect of the inertialess drie which causes some form of chaotic time compression, giving you the +-20% variations.. So there's still plenty of magic there.
Depending on either of the above scenarios depends upon whether or not things like 'beacons' or 'light-houses' would work, of course. The former - anything goes - the latter, I assume, would use normal electromagnetic radiation, and work just like modern radio lighthouses do - there's an old standard, which works, so it won't change.
As for signal language, Morse was around for way over 100 years without any change. The keys on the typewriter are probably going to be fixed while civilisation lasts (and yes, there's loads of sci-fi that mention the legacy), so signal transmissions tend to be rather stable, for all the reasons that you imagine. I think, even though Morse is now archived, if you were to send a distress signal in morse, you would still be using electromagnetic frequency, and people would still be able to work it out. Interplanetary emergency frequencies are far less likely to change over time, and there are always hobbyists listening out for 'old-school' style messages, especially considering the challenges of your space-flight.
As for upgrades and updates - technology is going to be distributed as fast as people can travel, since people can travel faster than light! LeGuin's "Dispossessed" features the invention and development of the first working Ansible - which allows for the many colony worlds to form a true federation for the first time, because they are suddenly able to communicate text, and later speech, in realtime (I love the book, but a huge plot-hole is that it assumes all planets are stationary in relation to each other, which is not true - so even ansible-voices should be reproduced with some form of doppler effect)