Maybe you should start a new project and make your own caius_top.v and we can take it one step at a time.
In your 'caius_top.v' module, since you will be placing the poorly named 'custom' module inside with the same port names, you should copy the port names at the top, where all you would change is the output reg to output, like so...
file 'caius_top.v':
`include "Verilog.v" // again stupid file name, but this is what you called it when you sent us 'verilog.txt'.
// Anyways, the include will tell Quartus to automatically add 'Verilog.v' which should be located in the same directory to your new project.
module caius_top( // this is your top module. Quartus should be told that this is your top module and your IO pins should be wired to the net names below.
input nRST,
input [7:0] D,
output wire [8:0] A,
output wire nDMA,
input nRDY,
output wire nBRQ,
input nBAK,
input BLTM,
input FLIP,
input [8:1] V,
input EINV,
input nHLD,
input HCLK,
output wire [9:1] H,
output wire HINT,
output wire nTR3,
input VFLP,
output wire [3:0] VLB,
input MATCH1,
output wire OUT54,
output wire OUT55,
output wire OUT57,
output wire [7:0] POS,
output wire [7:0] CHR,
output wire [7:0] ATR
);
// Instantiate module 'custom' from the source file 'Verilog.v' here...
custom custom_inst_1 ( // Again, this custom name of custom for your third party's logic is just silly...
.nRST ( nRST ),
.D ( D ),
.A ( A ),
.nDMA ( nDMA ),
.nRDY ( nRDY ),
.nBRQ ( nBRQ ),
.nBAK ( nBAK ),
.BLTM ( BLTM ),
.FLIP ( FLIP ),
.V ( V ),
.EINV ( EINV ),
.nHLD ( nHLD ),
.HCLK ( HCLK ),
.H ( H ),
.HINT ( HINT ),
.nTR3 ( nTR3 ),
.VFLP ( VFLP ),
.VLB ( VLB ),
.MATCH1 ( MATCH1 ),
.OUT54 ( OUT54 ),
.OUT55 ( OUT55 ),
.OUT57 ( OUT57 ),
.POS ( POS ),
.CHR ( CHR ),
.ATR ( ATR )
);
endmodule
Again, all I did here was make you a top module in your name directly wired to the 'custom' module from the file 'Verilog.v'.
Step 1 is just to get this to work just like it does now when the 'custom' used to be the top in your project.
Then, step #2 will be to cut a wire between the IO pins in your 'top', send that signal name through some custom logic like a PLL, then pass the output of that PLL to the instantiated 'custom' module below.