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I would just grab the logs and let the bike tell you what the fault was, in my experience all of the log lines are blissfully informative on issues.
I have had water issues on my '15 SR, but it was purely in the throttle, which is an off-the-shelf part and not really Zero's fault, but definitely did suck 

Let me brain dump since I'm going to eventually forget all of this

idk if they updated it since I last disassembled their android app in February 2017, but then it just downloaded onto your android device unscrambled (iirc to the storage directory so any other file explorer kind of app or any of the android debug tools should be able to read it), and even if you didn't want to grab it from an android device it was also easy to see the login pattern and grab the static authorization bearer and other expected HTTP headers to download the firmware.
e.g.
#grab an auth token
curl -v -H "Content-Type: application/x-www-form-urlencoded; charset=UTF-8" -H "Authorization: Bearer <snip don't want zero yelling at me too much>" -H "User-Agent: ZeroMoto/1.0" -d '{"email":""}' -X POST https://fupdater.zeromotorcycles.com/auth/login

#grab the firmware
curl -L -O -J -v  -H "Content-Type: application/x-www-form-urlencoded; charset=UTF-8" -H "Authorization: Bearer <snip don't want zero yelling at me too much>" -H "User-Agent: ZeroMoto/1.0" -H 'ZeroAPIAuth: <another snip don't want zero yelling at me too much>' -X GET "https://fupdater.zeromotorcycles.com/builds?currentversion&download=1"


which if you keep unpacking gets you files like this
75-08036-12_my17_mbb_firmware_banka_2016-10-26_160406.347.bin  75-08037-21_my17_bms_firmware_bankb_2016-10-26_155606.320.bin
75-08036-12_my17_mbb_firmware_bankb_2016-10-26_160406.347.bin  75-08118-15_zero_bootloader_2016-10-26_155428.128129a.bin
75-08037-21_my17_bms_firmware_banka_2016-10-26_155606.320.bin

The only other thing I remember being weird is they had an extra HTTP header that was a SHA-256 of the firmware tar.gz download, but it was called ZeroSha256 or something

I only really know the larger monolith batteries, but it seems likely to me that even the small fx packs also have their own bms-controlled contactors in them ( https://zeromanual.com/wiki/Unofficial_Service_Manual#Contactor ) that you will have to close.
I'd also note that at least on the larger monolith batteries, the battery module also has its own serial port that you can use to monitor balance, SoC etc, without having to go through the main bike board.

I'm not sure I'd recommend using the ZF3.3 packs in a car; they're small and somewhat light, but the maximum discharge C-rating for them is probably fairly low compared to what you want in a performance car relative to the battery size. (Or, if you're trying to use the tiny ZF3.3 module as the energy storage component of a formula-1 style KERS module to dump very high spikes of regen charging, the charge C-rating is also not great on these modules)
There are plenty of other battery cell chemistries that have much better maximum charge/discharge C-ratings that you could build a pack out of that are probably better suited to the application.

OP has the Hollywood Electric Elcon 2.5kW charger; it shows up on the MBB serial console as a recognized charger, does that mean it's okay and the BMS is still balancing etc? I guess I could examine the logs for cell voltage variance etc otherwise but I don't really want to 

I didn't realize that the new diginow 2.5s were so well-integrated. It wouldn't take too much arm-twisting at all to get me to sell these elcons and switch :-)
If you don't mind a semi-off-topic question, does the v2.5 diginow solution also correctly read the j1772 pwm pulse train and do correct current limiting automatically? I don't want to screw around with setting it manually every EVSE station I come to.

https://zeromanual.com/wiki/Unofficial_Service_Manual#Protections seemed to say that only works for 30 minutes, after which it opens again. Unless doing this kicks it fully into "charging mode" ?
I also need a solution that doesn't leave the key in the bike, since I use public chargers.

So you're saying all I need to do is to plug the external charger in, key the bike on, it sees that it's charging and kicks it into charge mode, and then when I key the bike off, it'll keep charging until it's done?

If so that's perfect.

I assume you live in Europe or you're really off-base with your cable choice 

The mennekes --> dual C19 adapter you linked is way overpowered and overpriced for your needs if all you really want to do is grab a single phase off of the Mennekes connector into a C13 connector.

If I were you, I'd probably get a [Mennekes] --> [1x C13 + 2x [C13 or C19] connectors for future quick charge adapters]; I have something similar that I use personally (mine is J1772 --> 1xC13 + 2x C19 with very different internal wiring because the united states is the worst and doesn't do 3-phase L2 AC charging).

If you are dead set on never owning any quick chargers, even a quick googling reveals tons of mennekes -> solo C13 connector plugs that are cheaper ( https://www.laadkabelfabriek.nl/product/laadkabel-type-2-male-naar-c13-apparaatstekker/ was the first one I happened to see)

(I recently replaced my 2015 SR DC-DC 12V converter in this thread http://electricmotorcycleforum.com/boards/index.php?topic=7981 )

Yes, you can use the higher spec'd unit as a drop-in. Your bike doesn't need the higher wattage, as it doesn't have peak-power-hungry ABS pumps that later bikes have, but you won't hurt anything and the individual circuits will remain correctly fused at their own amperages.

If you can, testing the DC-DC converter on a bench power supply and multimeter is informative, at least for my own case; I'm pretty sure most of my own issue turned out to be moisture ingress causing intermittent shorts in the 12V system.

Good luck in general, the 12V converter is smack-dab in the middle of the bike and is annoying to deal with.

I ended up making my own ( http://www.thingiverse.com/thing:1764732 )