This is the voltage regulator should be attached somewhere close to the battery. https://www.amazon.com/Caltric-REGULATOR-RECTIFIER-KAWASAKI-Prairie/dp/B00KOR3JXY/ref=sr_1_1_sspa?crid=27BKH1Y3WPA0N&dib=eyJ2IjoiMSJ9.Mq6Eg3h1J_je8whkUrN6dwAzcF5Qf_kHQP171pYHemg-l3gKjB9c5Pe9QGfR9GBSWBnYiUn2glWcq7Diy6aJKs--SKZRJ8q1QNxSOgDNRZUj3lC7OhNCPCV1CCAhyA44ZbGra_iqFhc2rFaOLDLfj9qjEGjfG4UWalygLMlILa6Xhr44xA6Smw9he_53GlSMbwpizuibaZj73qMuYMD0mjzJVj9PwDMAui4s8SMfH2wuXdqSamZ39DNXRi_1YrgLkwDg-SCmeC4xsNIxQ2Bfk5Wg7gd-qYk9-gpY4LDjIng.KyPXdGVHDTH2GtpMI6_zf2JYX9R33BqmOQZuFcDKing&dib_tag=se&keywords=1997+kawasaki+prairie+400+voltage+regulator&qid=1747844997&sprefix=1997+kawasaki+praire+400+voltage+regulator%2Caps%2C131&sr=8-1-spons&sp_csd=d2lkZ2V0TmFtZT1zcF9hdGY&psc=1

The original breakdown sounds like a battery and charging problem. Was it the voltage regulator you replaced ? Have you checked the fuses ? I'd be checking the charging.. the bikes earths and power wires. Check the cdi has a good earth and a power supply if it is meant to have one. Get the service manual and it will say how to check the charging, and the ignition..

Thats the stator, the pickup coil is attached to it on some bikes, but not yours. It appears to be separate. That part is for battery charging. The pickup coil causes the plug to fire when the magnet on the rotor goes past it. It is under the crankcase cover but before you tear into that there are tests you can do with the meter to determine if it is bad. It tells you in the service manual the correct resistances for a good coil, its possible neither are bad. This is the pickup coil: https://www.amazon.com/Pick-Up-Kawasaki-1997-2002-183-2065-59026-1110/dp/B084RJ952X/ref=sr_1_3?crid=39CT0V21SUK9M&dib=eyJ2IjoiMSJ9.bFaF7gjMjq2Jdo4FwLE89SGxsiS7hiv5zZ5QUztKizbTm_nsJ_f5nbiAM5rQm_UcHDVAMP70mJF9ERZB4uZ7780IqPo-Dv9ow25V5ZOFpKdWe7E0BEsMw6LwTz2H5r4fQgUPknEJTBeYzayE5267y9YABFdPS6gzYKYx4Yj-oZ0pbGkqLc6jdLZVOw5wGQ_tsTi_wHXxwJ5O0nhyltMg-iqR2Pu0MRtq8OGWGwz7zxpfH7u9z9YWXaRrP9C74GK-TsWZMMduDnx8Fe4DD9NEykTspOvSq2ooX0toGtq-c8c.rOhv1-yXT8aF1L9Ydu7GudOkQ_6yC8_98g9JmnItCos&dib_tag=se&keywords=97+kawasaki+400+pickup+coil&qid=1747796344&s=automotive&sprefix=97+kawasaki+400+pickup+coil%2Cautomotive%2C114&sr=1-3 You can unplug it from the harness and check the resistances and also check to make sure its putting out voltage as you rotate the engine, that is best done with an anologue meter the needle is more sensitive to small voltage spikes but its fast you have to look closely or you will miss it.

The only thing you havent replaced is the stator and pickup coil i might look in that direction something caused this wheather it was a loose ground poor conection somewhere or voltage spike. Check to make sure your CDI has good voltage supply and ground . Battery swelling up sounds like a charging problem might also check the voltage regulator.

I couldn't tell you the difference but we had a Quadrunner when I was a kid. It smoked like crazy and dad always used to say "at least it kills the mosquitoes ". Them were the days.