PIC32 Issue with using JTAG Pins as Analog Inputs
So I had to re-read through the ADC document and ask for some help, but I think I've found the way.

My previous iteration used a method of defining certain parameters, but I ended up just doing direct assignment to the registers eventually.

For anyone else with the same problem, the following is my code:

Configuration for analog:

DDPCONbits.JTAGEN = 0;
TRISB = 0x1111;

IFS1CLR = 2; //clear ADC conversion interrupt
IEC1SET = 2; //enable ADC interrupt
AD1PCFG = 0x0000; //Configure all input pins to Analog
AD1CON1 = 0b00000000000000001000000011100110; //Configure Sample clock source
AD1CON2 = 0b0000010000100000; //Configure ADC voltage reference

AD1CON3 = 0x0000; //Configure ADC conversion clock
AD1CON3bits.SAMC = 0b00001;    //auto sample at 2TAD
AD1CON3bits.ADCS = 0b00000001; //TAD = 4TPB
AD1CHS = 0x00000000; //Configure input channels- CH0+ input,

AD1CON2bits.CSCNA=1;
AD1CSSL = 0b0001001111111100;
AD1CON1SET = 0x8000; //Turn on the ADC module


Then, for acquisition, I call this method within an ISR on a timer of ~half a second:

void getAnalog() {
while( ! IFS1bits.AD1IF); //wait until buffers contain new samples
    AD1CON1bits.ASAM = 0;     //stop automatic sampling (shut down ADC basically)

    vt1 = ADC1BUF0*.003185;
    vt2 = ADC1BUF1*.003185;
    vt3 = ADC1BUF2*.003185;
    vt4 = ADC1BUF3*.003185;
    mosVolt = ADC1BUF4*.003185;
    Battery_volt = ADC1BUF5*.003185;
    vt5 = ADC1BUF6*.006125;
    vt6 = ADC1BUF7*.006125;
    Csensor_volt = ADC1BUF8*.006125;


    IFS1bits.AD1IF = 0;
    AD1CON1bits.ASAM = 1;  //restart ADC and sampling
}


Variable names and scalers on each may vary.