You will want to edit keymap_common.h to match the physical layout of your matrix.
// JCK: Semi-Standard layout
#define KEYMAP_JCK( \
K00, K01, K02, K03, K04, K05, K06, K07, K08, K09, K0A, K0B, K0C, K0E, \
K10, K11, K12, K13, K14, K15, K16, K17, K18, K19, K1A, K1B, K1C, K1D, K1E, \
K20, K21, K22, K23, K24, K25, K26, K27, K28, K29, K2A, K2B, K2D, K2E, \
K30, K31, K32, K33, K34, K35, K36, K37, K38, K39, K3A, K3C, K3D, K3E, \
K40, K41, K43, K46, K4A, K4B, K4C, K4D, K4E \
) { \
{ KC_##K00, KC_##K01, KC_##K02, KC_##K03, KC_##K04, KC_##K05, KC_##K06, KC_##K07, KC_##K08, KC_##K09, KC_##K0A, KC_##K0B, KC_##K0C, KC_NO, KC_##K0E }, \
{ KC_##K10, KC_##K11, KC_##K12, KC_##K13, KC_##K14, KC_##K15, KC_##K16, KC_##K17, KC_##K18, KC_##K19, KC_##K1A, KC_##K1B, KC_##K1C, KC_##K1D, KC_##K1E }, \
{ KC_##K20, KC_##K21, KC_##K22, KC_##K23, KC_##K24, KC_##K25, KC_##K26, KC_##K27, KC_##K28, KC_##K29, KC_##K2A, KC_##K2B, KC_NO, KC_##K2D, KC_##K2E }, \
{ KC_##K30, KC_##K31, KC_##K32, KC_##K33, KC_##K34, KC_##K35, KC_##K36, KC_##K37, KC_##K38, KC_##K39, KC_##K3A, KC_NO, KC_##K3C, KC_##K3D, KC_##K3E }, \
{ KC_##K40, KC_##K41, KC_NO, KC_##K43, KC_NO, KC_NO, KC_##K46, KC_NO, KC_NO, KC_NO, KC_##K4A, KC_##K4B, KC_##K4C, KC_##K4D, KC_##K4E } \
}
The bottom section names each matrix position. The top assigns those positions to the keymap. You probably just need to rearrange the gaps in your matrix.
I think.