Basic setup in Quartus

You need to instantiate your Nios in the top.v for your new development board. I've done so as an example below.

It looks like your new board has a 50MHz oscillator on it, this is common. So, there's (probably) no need for your PLL. I've removed and just fed your Nios with the 50MHz clock.

LED connections are straightforward. I've assumed SEL1-3 are switches on your new dev board (I don't recognise the I/O signal list you posted - which development board is it for?). If they're not you'll need to substitute in signals that are switches (or push buttons perhaps?).

I'm not sure why your Nios module would need the 10MHz clock and you should be able to ignore the PLL locked signal you had before - see comments in code.

I've not compiled the code - it's just provided for guidance. Let me know how you get on.

Cheers,

Alex

module top
(
// {ALTERA_ARGS_BEGIN} DO NOT REMOVE THIS LINE!
    ADC_7,
    ADC_8,
    ADC_PSB1,
    ADC_PSB2,
    ADC_PSB3,
    ADC_PSB4,
    ADC_Vc1,
    ADC_Vc2,
    BP_SW_1,
    BP_SW_2,
    CLK50M,
    EXT_ADC1_CLK,
    EXT_ADC1_CS,
    EXT_ADC1_DATA,
    EXT_ADC2_CLK,
    EXT_ADC2_CS,
    EXT_ADC2_DATA,
    GD_FB,
    LED,
    LVDS_det,
    LVDS_RD_MINUS,
    LVDS_RD_PLUS,
    LVDS_TD_MINUS,
    LVDS_TD_PLUS,
    PSB_ENA,
    PSB_FAIL,
    PWM_S,
    RS232_CTS,
    RS232_RTS,
    RS232_RX,
    RS232_TX,
    SEL1,
    SEL2,
    SEL3,
    TEMP_CAP1,
    TEMP_CAP2,
    TEMP_PCB,
    TEMP_SW,
    xBP_SW_1,
    xBP_SW_2,
    xEXT_ADC1_CLK,
    xEXT_ADC1_CS,
    xEXT_ADC1_DATA,
    xEXT_ADC2_CLK,
    xEXT_ADC2_CS,
    xEXT_ADC2_DATA,
    xGD_FB,
    xPSB_ENA,
    xPSB_FAIL,
    xPWM_S,
    xTEMP_CAP1,
    xTEMP_CAP2,
    xTEMP_SW
// {ALTERA_ARGS_END} DO NOT REMOVE THIS LINE!
);
// {ALTERA_IO_BEGIN} DO NOT REMOVE THIS LINE!
input            ADC_7;
input            ADC_8;
input            ADC_PSB1;
input            ADC_PSB2;
input            ADC_PSB3;
input            ADC_PSB4;
input            ADC_Vc1;
input            ADC_Vc2;
output           BP_SW_1;
output           BP_SW_2;
input            CLK50M;
output           EXT_ADC1_CLK;
output           EXT_ADC1_CS;
input            EXT_ADC1_DATA;
output           EXT_ADC2_CLK;
output           EXT_ADC2_CS;
input            EXT_ADC2_DATA;
input       GD_FB;
output      LED;
input            LVDS_det;
input            LVDS_RD_MINUS;
input            LVDS_RD_PLUS;
output           LVDS_TD_MINUS;
output           LVDS_TD_PLUS;
output           PSB_ENA;
input            PSB_FAIL;
output      PWM_S;
input            RS232_CTS;
output           RS232_RTS;
input            RS232_RX;
output           RS232_TX;
input            SEL1;
input            SEL2;
input            SEL3;
input            TEMP_CAP1;
input            TEMP_CAP2;
input            TEMP_PCB;
input       TEMP_SW;
output           xBP_SW_1;
output           xBP_SW_2;
output           xEXT_ADC1_CLK;
output           xEXT_ADC1_CS;
input            xEXT_ADC1_DATA;
output           xEXT_ADC2_CLK;
output           xEXT_ADC2_CS;
input            xEXT_ADC2_DATA;
input       xGD_FB;
output           xPSB_ENA;
input            xPSB_FAIL;
output      xPWM_S;
input            xTEMP_CAP1;
input            xTEMP_CAP2;
input       xTEMP_SW;
// {ALTERA_IO_END} DO NOT REMOVE THIS LINE!
// {ALTERA_MODULE_BEGIN} DO NOT REMOVE THIS LINE!
// {ALTERA_MODULE_END} DO NOT REMOVE THIS LINE!
wire       nios_50M_clk;
wire       reset_n;
wire  LED_ctrl_from_nios;
wire  SW_to_nios;
assign nios_50M_clk = CLK50M;             // Local 50MHz osc on your new board means you don't need your 10MHz->50MHz PLL
assign reset_n = 1'b1;                    // Just tie reset_n high to take Nios out of reset from the start
assign LED = LED_ctrl_from_nios;     // Connect 3 LEDs to your control from your Nios
assign LED = 5'b0;                   // Tie off unused LEDs
assign SW_to_nios = {SEL3, SEL2, SEL1};   // A guess, assuming SEL1-3 are switches on your dev board. If not you will need to find some.
         // Instanciate your Nios module inside the outer 'top' wrapper module for your new dev board.
   nios_setup u0 (
      .clk_clk                               (nios_50M_clk),         //                            clk.clk
      .reset_reset_n                         (reset_n),              //                          reset.reset_n
      .led_io_external_connection_export     (LED_ctrl_from_nios),   //    led_pio_external_connection.export
      .sw_io_external_connection_export      (SW_to_nios),           // switch_pio_external_connection.export
            // Suspect you don't need the following two lines for your application. Either tie off (as below)
            //   or revisit in Qsys and modify your component to remove them.
      .modular_adc_0_adc_pll_clock_clk       (1'b0),                 //    modular_adc_0_adc_pll_clock.clk
      .modular_adc_0_adc_pll_locked_export   (1'b0)                  //   modular_adc_0_adc_pll_locked.export
    );
endmodule