They have lots of "drop in" lithium batteries, i.e. 2 lbs, 12v, 14ah:
Amazon.com: Shorai LFX14L2-BS12 Extreme Rate Lithium Iron Powersports Battery: Automotive
If you are bent on 30 year old technology then I don't know what to tell ya. Also I'm not sure what ECU you are referring to since you are talking about a plane one minute then a prius the next. I don't know why the ECU can't be disconnected (or the whole battery) in either event, or if it is custom arduino why data can't be stashed on eeprom on shutdown.