Some issues I've found:
New N145 branch at Gobara?
New N353 branch at Shibukawa
E29 and N373 don't intersect properly
E35Kar and N202Ima don't intersect properly
KE2 and N199 don't intersect properly
New piece of E55/N493 east of E55Tan?
N1 interchange between N139 and N139FIS, KanBarE and KanBarW, P208 and P81/P381, N1Nis_E and N1Nis_W, P44_Iwa and P262 (two), P262 and N152, N152 and N150
N1: N23Mei -> N23, N23/N259 -> N151/N259, N1Kei/N478 -> N1Kum/N478
N1: what is the E23 point supposed to be?
N1 missing point for E1(33-1)
N1DKR interchange between P188 and E89(1), E89(5) and NagHig, N170 and E89(11)
N1DKR: N1Kei -> N1Kum
N1Hok interchange between P66_E and P66_W
N2 and N28 should not overlap HE3
N2 interchange between HE3(3-23) and N28_W, N29 and N179_W, N179_W and P29_B (three), P29_B and P44/P715 (five?), E2(11) and N250/N374, P37 and P397 (three?), P397 and P45 (three), P40 and N30 (two?), N30 and P21_B, P21_C and P73, P22_B and N429_N (three), N429_N and P54, P54 and ToN429 (two), P54_E and N2Ono_E (three), N2Ono_W and P55, P25_Hir and P50/P362 (three), N375 and P67_B (four), N2EH_W and P86 (three)
N2Ono interchange between N2_E and P48, E76(1) and N184, N184 and N2_Fuk (two), P71 and P41_Hir (two), P41_Hir and N2WH_W, N188_W and E2(37) (two?), P58 and P24 (two?), N9_E and N190_E, N190_E and E2/P6, E2(45) and N190_W (two)
N2: P90_W relocated
N2WH interchange between N2 and P71, P71 and P41 (four), E2 and N2_W
N2 has a branch from P335 to
E2Is N2Kan signed?
N3Kur: End -> KE5 (and it seems that logically it should use the ramps back to N3)
N3 interchange between N199 and P73, P27 and P87 (four?), P87 and P69 (three), P75 and P92, P92 and P97, P97 and P30, KE2(209) and P35_S (two), P31 and N200_S (two), N200_S and P17, P17 and N34
N3Hak interchange between N3_N and N201
N3Kum interchange between N3 and N387, N387 and P49, P49 and N57
N3Kag interchange between E3_Kag and P24
N4 interchange between MeiDor and SEC2/P308, SEC2/P308 and P318, P49 and P34, P34_Nas and P17 (two), P17_Kor and P47 (two), P47 and P6, P6 and N49, N49 and N288 (four), P30_Ota and N459_W, N459_E and P62_Nih, P62_Nih and P39/P129 (two), P51 and N115_W (four?), P23/P137 and N45, N45 and P8, P56_N and N347/P1 (two), P1_N and E4(32), P48_Kur and N284/N457, N4Miz and E4(36), N281_End and N282/P16 (two), E4(43) and P157, P6_Nin and P24_Nin, N454_W and N45/N102
N4Uts interchanges between C4 and N354 (two), N354 and P56, P56 and N125, N125 and P54, P54 and N50, N50 and P44 (four), P44 and N352/P47 (four), P35 and E50, P46 and N123
N4 should have a point between P126/P127 and P54_Sen for the connection to E48
N6 interchange between N298 and N464, N16 and P7_A, P8 and P11, P19 and N6UsS (three), N354/N125Ami and P24 (two), P24 and N125 (two), N125 and P64, P43_S and P43_N, P38_A and P31_N, N289 and P10_N, Ona and P66 (three?), N49 and P26, P26 and N399 (three), P36_B and N288, P266 and N115/P74, N115/P74 and P38_B (two)
N7 interchange between P46 and P556, P53 and N113?, P38_N and N47/P40, N345_D and N345_E, E7(12NTE) and P32 (two), N341_E and P44_Iwa, P65_S and P65, E7(15) and P3_Fut, P3_Hir and P41, N7Aom and N280Uch, N280Uch and N280
N7Aom interchange between N7 and E4 (two), E4 and P44_N
N8 interchange between P20 and E8(38), E8(38) and P8, P8 and N17/N351, P53 and P52, P68 and N41 (two), P1 and P41_Toy, P41_Toy and N472 (two), P11_Imi and P24 (two), P32 and N471, P16_Oya and P59 (five), N159_N and N159_S (eight), N8Ima and E8(17), E8(17) and P60 (two), P58 and N305_N (six), P54 and N360, N416/P22 and P11_Kom (three), P11_Kom and N305, N305/N364 and P61_Kag, N416 and N158 (two?), N158 and P32_Fuk
N8: N8BypOts -> N1Ots
more to come