So I just got my lsj back on the streets from doing an engine swap. everything is running great except one little detail. I thow a "random misfire code" every now and again. Ive read that the check engine light flahses when it senses misfire. The check engine light flashes only when I am decelerating and engine breaking (downshift to use engine to slow down) and in either 2nd or 1st gear. If i just hold in the clutch and use the break 100% to slow down, the check engine light does not flash. When i accelerate or am at cruising speeds, the check engine light does not flash. I realize that this is a very specific problem but any help would be greatly appreciated.

Mods are,
zzp gen lll shortblock
stage 3, 2.8, 60#, 2 step colder plugs, lightweight flywheel, zzp 3 inch header back exhaust