You might need the crossovers from the aftermarket speaker set actually.
Note: If your 2009 is one which had a powered amp - the following may not apply.
So I did up this How-To ages ago
HOW TO: FD Body - Remove/Replace/Swap OEM (2DIN) headunit when I had an 2010 FD i30cw (aka Tourer) - while the pinout is for an Australian specific OEM unit from 2011 - it was a drop-in replacement
(i.e no re-wiring at all) for the 2010 OEM unit (which I believe was multi-country).
In other-words... the FD-01 pinout, at least for the audio side of things, may likely be the same as your head-unit... assuming it is OEM (and you don't have the OEM amp). Your mileage may vary, etc., etc.
Which brings me to this point
I don't see any tweeter connections on the head-unit pinout (albeit FD-01) - so I would think the OEM tweeters are connected in similar manner as your after-market is intended to be.
Which almost certainly would be in parallel across the woofer connection (of course being OEM wiring harness they could have done that anywhere from the head-unit to the OEM woofer). I think we will actually find that the cap on the OEM tweeter is actually a part of the 'cross-over' circuit - i.e. High Pass Filter - the parts don't need to be right next to each other. In your JL kit - it would appear the HPF components are all in the separate little box on the cable instead.