Thanks for the code, it already scares me.
The Arduino programming IDE makes things easier, but, you'll still need some programming skills. We (probably) won't write your program for you, but we can sure help.
RTC (i2c, says ds1307 based)
If your budget can support it, consider the DS3231 as it uses the same software library but is more accurate.
is there any drawback picking a Nano/Mini/Micro over a bigger board?
Well the Nano has USB on board, so it's plug'n'play for programming it. The Mini/Micro, on the other hand, requires a USB-serial adapter to program it. Since you're probably not going to need to program it after you finish debugging, this is probably not a big issue. But selecting a 3.3V board (i.e., not the Nano) is ideal as it makes talking to the SD card easier.
If my choice of hardware is complicating the coding than I'd rather swallow the bitter pill of getting an Uno or the like in a case outside teh bike.
No problem, using a Mini or Micro will not change your code BUT the SD card library is rather big (13KB!) so you will want to make sure you get a 32KB (Atmega328P) Mini/Micro and not the 16KB version.