Parts removed

R31, R32,R33 ... R62, (200R)
R78,R79 ... R93, (4K99)
U47 (SN65LVDS048AD)
C64 (10nF)
R215 (33R)
R107 (33R)
U4 (NC7SP74K8X)
R103 (10K)
R7 (330R)
C66 (10nF)
C65 (10nF)
U50 (NC7SZ126P5X)

Parts added

C64 ... C66, C219 ... C230 (100nF 0603, place next to U29 ... U44)
V133 (SI2323DS-T1-E3, place next to J10)
R7 (10K 0603, place next to V133)
L72 (742792096, at start of the P3V3A power plane)
C231 (100nF 0603, at start of the P3V3A power plane)
V134 (schottky diode 100V,3A, SK310A-LTP, place near to F1)
R31 (varistor 26V, 800A, VJ14M00200KBA, place near to F1)

Part value changed

R109: 220K->47K
U29 ... U44: SI8540-B-FW -> INA193AIDBVT
R15 ... R30: 0.1R -> 0.05R
U5: DS92001TLD -> DS92001TMA (SOIC-8)
U52: AD5601BKSZ -> AD5621AKSZ

FPGA, pins swapped

H4 -> J3 (L2_TRIG_P)
H3 -> J1 (L2_TRIG_N)
K3 -> H4 (BP_ADDR(2)
J4 -> H3 (BP_ADDR(3)
G3 -> K3 (BP_SCLK_P)
G1 -> J4 (BP_SCLK_N)

FPGA, bank_1 (C21, E19, G21, J18, L16, L21, N18, R21, U18, W21)

VCCO_1_1 ..1_10, P2V5 -> P3V3
C36 .. C44, P2V5 -> P3V3


Nets removed

CTDB_CUR_N
CTDB_CUR_P
CUR_P1 ... CUR_P15
CUR_N1 ... CUR_N15
SCK_R
DIN_R
M1
nM1
nCS
nCFG_EN
nRST

New nets

P3V3A (power plane, possibly embedded in other power plane)
nLED_ENA (U1-A4)

Schematic correction 
(last CTDB1 backannotion was missing, CTDB1 schematic is wrong here)

see swapped PPS_BUSY_P(1),_N(1) / PPS_BUSY_P(4),_N(4) at R142, R126, R134