that's sounds great, i think the ESP32-S3 internal pull-up/pull-down resistors are usually 45k Ohms. How are you testing the BM1397 chip on the board ?
my bringup plan;
1. make sure I2C is working (done)
2. Make sure the DS4432U+ is alive (done)
3. Adjust the BM1397 core voltage to 1.5V with the DS4432U+ over I2C from the ESP32
4. Test the BM1397 with cgminer using the level shifted J6 debug header and a USB Serial cable
5. make some ESP32 FW to test the BM1397 from the ESP32
then..
6. Make proper drivers for the DS4432U+, EMC2102, INA260, and LEDs
7. Make sure the ESP32 can connect over WiFi (done)
8. Get stratum work from ckpool
9. Format work for the BM1397, and send it to the BM1397
10. send stratum responses
11. Mine BTC!
Can you upload that small testing code that you have or use to the github repo for testing . i have managed to have the wifi connection done. Just started working on I2C