I'm not sure I correctly interpreted your intended API on bit_set_seq(), and I know I didn't on bit_set_skip.

For bit_set_seq(), I interpreted the index to the array-ref as the bit number of the output, and the value at that index as the bit number for the input. If you intended the other way around, my tests below should work for exp0123 and exp3210, but won't be right for exp0312. But since my tests are completely failing, there's probably something I'm missing about the way you intended it to be used.

use Bit::Manip qw(:all);
use Test::More;

# out of order sequence
my @exp0123 = (0..15);
my @exp3210 = reverse(0..15);
my @exp0312 = (0b0000,0b0001,0b0100,0b0101,0b1000,0b1001,0b1100,0b1101
+,0b0010,0b0011,0b0110,0b0111,0b1010,0b1011,0b1110,0b1111);

for (0 .. 15) {
    is( bit_set(0x00, 2, 4, $_), $_ << 2, "nomal set, shifted up 2" );
    is( bit_set_seq(0x00, [0,1,2,3], $_), $exp0123[$_], "[0,1,2,3]: I 
+expect bit 0 [LSB] of input to be transferred to bit 0 [LSB] of outpu
+t -- ie, same order");
    is( bit_set_seq(0x00, [3,2,1,0], $_), $exp3210[$_], "[3,2,1,0]: I 
+expect bit 3 [MSB] of input to be transferred to bit 0 [LSB] of outpu
+t, in2 -> out1, in1 -> out2, in0 -> out3 -- ie, reverse the bits");
    is( bit_set_seq(0x00, [0,3,1,2], $_), $exp0312[$_], "[0,3,1,2]: I 
+expect in0 -> out0, in3->out1, in1->out2, in2->out3");
}

... # your subs go below, not quoted here...
[download]

For bit_set_skip, I couldn't interpret it at all... What I would want would be a feature where I could put arbitrary gaps, for example, $out = bit_set_skip( $in, $seq, $val ). I would want to break $val into chunks based on seq, and put it into $in to create out. For this table: K means "keep the same bit value as in input", whereas a 1 or 0 means that I want that value there, regardless of what was originally in INPUT. I couldn't figure out the $seq necessary to do this, but below my table is the API I would have guessed to set this...

#       INPUT           VAL             DESIRED OUTPUT
#       0bKKKK_KKKK     0b0000_0000     0bKKK0_K000
#       0bKKKK_KKKK     0b0000_0001     0bKKK0_K001
#       0bKKKK_KKKK     0b0000_0010     0bKKK0_K010
#       0bKKKK_KKKK     0b0000_0011     0bKKK0_K011
#       0bKKKK_KKKK     0b0000_0100     0bKKK0_K100
#       0bKKKK_KKKK     0b0000_0101     0bKKK0_K101
#       0bKKKK_KKKK     0b0000_0110     0bKKK0_K110
#       0bKKKK_KKKK     0b0000_0111     0bKKK0_K111
#       0bKKKK_KKKK     0b0000_1000     0bKKK1_K000
#       0bKKKK_KKKK     0b0000_1001     0bKKK1_K001
#       0bKKKK_KKKK     0b0000_1010     0bKKK1_K010
#       0bKKKK_KKKK     0b0000_1011     0bKKK1_K011
#       0bKKKK_KKKK     0b0000_1100     0bKKK1_K100
#       0bKKKK_KKKK     0b0000_1101     0bKKK1_K101
#       0bKKKK_KKKK     0b0000_1110     0bKKK1_K110
#       0bKKKK_KKKK     0b0000_1111     0bKKK1_K111
for (0 .. 15) {
    is( bit_set_skip( 0x00, [0,1,2,4], $_), (($_ & 0x08)<<1) | (($_ & 
+0x07)<<0), "put a gap between the MSB and the lower three bits");
}
[download]