00-02 Rodeo 4L30e have a different electrical connector configuration than 99 and older 4L30e, so the 00-02 is not plug and play.
A 96 4L30e 4WD should interchange with a 98-99 4WD 4L30e, but being a JDM there could be a difference in the electrical connections as well. Do you have a link to the JDM 4L30e?

 

Got it right here

JDM Honda Passport V6 3.2L 4wd Automatic Transmission 1994-1997

JDM Used Engines and Transmissions - Lynnwood, WA Seattle, WA

shop.foreignengines.com

 

The electrical connectors seem to be correct. A round 5 pin on the Overdrive section and a square 4 pin on main case.
This transmission even has a dip stick.
It is unclear how the shift cable is retained to the Bell housing, compare to your 98
I am reasonably sure this transmission will work in your truck if the e shift cable will attach.

 

Click on the image to expand

 

I didn’t see an attachment for the shift cable on the spare 98 core I have (that should be identical to what’s currently in my truck). I’m also wondering about the trans mounts or speed sensors, would those still be compatible? I’d assume the sensors stay the same since it’s the same part number

 

This is how the cable is secured on late model Rodeo/Amigo

 

The cable clamp is bolted to these threaded bell housing mounts.
How is the cable attached on your 98?
Does the JDM 4L30e have the threaded mounts?

 

I found the same threaded mounts on my 98. It looks like the cable threads into the same spot on photos of 96-97 as the 98 core I have. Should I worry about transmission mounts? Will I need a 98 torque converter? Are all electronics the same?

 

On your JDM link there is a phone number, I would call them and ask them directly what the differences are and I suspect they could tell you, as well as while you are calling, you could also ask if they have one specific for a 98 Rodeo and the cost if they do have one.

 

How many miles on the JDM transmission?
The mount on your installed transmission should fit the JDM
The electrical components should be the same.

 

Website says their transmissions average 50k, I’ll ask for exact mileage and pictures when I call to order it. Even if the actual mileage is higher, a year warranty at that price is too good to pass up if it’ll work. Anything else I should double check before ordering it?

 

Ask about the shipping cost.