Heres another idea. Before the loop starts load 0 into d5, and d6. If an 8 bit value needs to be used as 32 bits, load it into d5. If a 16 bit value needs to be used as 32 bits load it into d6.

adc_indx:
move.b (a3)+,d5
add.b d3,d5
lea.l 0(a4,d5.l),a0
move.b (a0)+,d1
move.b (a0),-(a7)
move.w (a7)+,d6
move.b d1,d6
move.b 0(a4,d6.l),d0
add.b d7,d7 ;maybe set extend flag
addx.b d0,d2
scs d7
svs (a2)
move.b d2,d5 ;N
move.b d2,d6 ;Z
bra.l update_timer