Found the problem - dead or dying ECM. Before I got involved in the project, the air meter was hooked up with 12 volts on the signal return or one of the wires, not sure, but our theory is that the 12 volts killed the ecm. What puzzles me is how the car still ran?
We put a known good LA3 ecm in this morning and the car immediately acted different. The fuel pump actually primed and then shutoff - it had been just staying on. It fired on the first hit and ran at fast idle and then eventually bumped down. It now boosts fine without breaking up and the timing is advancing when its supposed too.