So, I'll be replacing my front door speakers shortly with another component set and I was wondering how the crossover duty is handled with the stock JBL stuff. Is there simply a speak lead that comes into the doors I can run to my new components included crossover or are there 2 separate leads for the mid and tweeter?

Just as an FYI, I recently had a front door speaker blow and researched all the options of replacement. replacing the doors with components, replacing the whole system, getting a new head unit etc.. etc..

In the end because I wanted to keep the stock HU and sub I wanted to find replacement speakers that matched existing as best possible, since most aftermarket 4ohm speakers would not match up with the rest of the existing JBL system

I ended up buying PowerBass 2ohm 6.75" for the front doors, and PowerBass 2ohm 6.5" speakers for the rear doors. I installed the one 6.75" speaker in the door that was damaged and nearly stopped there, but I ended up installing all 4 and the system sounds great again.

Not sure what you are going for with your system build, but unless you're planning on ripping out the HU and get a new amp for a replacement sub I cant recommend these affordable 2ohm speakers I installed. link below.

Rear Doors
PowerBass L2-652 6-1/2" 2-way car speakers — for use with 2-ohm factory systems at Crutchfield

Front Doors
PowerBass L2-675 6-3/4" 2-way car speakers — designed to replace 2-ohm factory speakers at Crutchfield

I have the JBL system with an aftermarket headunit. Are 2ohm speakers what I should be looking at in regards to replacing?

Also, any reason you went with the 6.5 vs a 6 x 9 in the front? I see this option for a 6 x9 PowerBass L2-692T 6"x9" 2-way car speakers — designed to replace 2-ohm factory speakers at Crutchfield

If you have an aftermarket head unit than you're likely bypassing the factory amp? If you are than installing 4 ohm speakers may not be an issue, if you're running the factory amp that powers the existing speakers than 2 ohm speakers will be a direct replacment.

Honestly, I saw those 6x9's after i already had my new ones installed, I would ask crutchfields if those would be a direct replacement fit for the 4runner. could be that the cut out is a little funky and may need you to trim something so they wont recommend it or they should be able to tell you if it fits.

Unfortunately, I have no idea if it bypasses the factory amp. I purchased the car used and the PO installed the Alpine back in 2006 a few months after the car was purchased. $2000 unit price! It's crazy to look back at how much audio products were 15 years ago.