The four pins on the RJ45 jack shouldn’t be the problem — they are for the two LEDs on the RJ45 jack, so not connecting them merely causes the LEDs to remain off and shouldn’t matter with the power circuitry. Since your VIN to GND resistance is still very low (29 ohm as you described), it suggests that there is still a shorting / damage somewhere on the VIN line. Try yo remove IC1 and see if that changes anything.