Has anyone ever done an Ultegra Di2 upgrade?
I’ve done an installation, so kinda?
Is it a nightmare to do?
No. Actually looks like you might be ok, looking at the R3 manual; there are no obvious gotchas. Looks like it might be a solid BB shell and you access the guts of the bike from a port underneath it. Wiring diagram looks straightforward: https://www.cervelo.com/media/gene-cms/r/3/r3_disc_manual.pdf
One caveat about the wiring in the next section though…
Also see if you can get the Cervelo specific port covers mentioned in the manual though. Dunno if they have a spares website.
Do i need lots of special tools?
Di2 specific tools are limited to that plastic doohickey that you use to connect the wires and this came with my groupset (also I think it costs about £3 separately, thank goodness). What I think you’ll need in addition from looking at the wiring diagram is a routing kit e.g. IR-1.2 Internal Cable Routing Kit | Park Tool which is the one I use and it is 
You’ll probably want to bleed your brakes after swapping the levers over, you’ll probably lose a little oil. Ultegra R8070 needs an additional part on top of the standard bleed kit like this: Shimano ST-R9120 Funnel Adapter and O-ring | Tredz Bikes but my levers came with one of these.
Is it worth it?
Electronic shifting is great. I also found it quite fun to build. It’s hard to say whether it’s worth the few hundred on top of a mechanical road group with STI shifters though. On my TT bike with a non-indexed front bar-end shifter though, I would sell my soul to get rid of that bloody thing 