Let's review the cam and IP timing.

When the engine is turned by its crank, not its cam, to the point where
the notch in the thrust collar is aligned with the groove cut into the
left front cam support, you say the reading on the harmonic damper is 00
degrees. Good.

You say the IP timing is a bit retarded at 3 degrees. I'm puzzled by
that. How are you measuring that?

The start of delivery should begin at 24 degrees (+/-  1 degree) BTDC.

Given the engine's recent history and these symptoms, I suspect that
your IP timing is, in fact 27 degrees retarded; that would well account
for the poor fuel economy and cause lame acceleration.

If this is the case, to correct the IP's timing, the engine should be
turned to 24 degrees BTDC BEFORE the IP is removed. The IP's drive gear
has an intentionally missing tooth. That gap should be aligned with a
groove cut into the collar immediately behind the IP's drive gear and
the pump reinstalled. The IP's mounting flange is designed to allow
small adjustments while the IP is on the engine - turning toward the
engine advances the timing, away retards.

The ALDA is tied into the turbo's boost pressure and adds fuel at high
engine loads - acceleration. Pray that your ALDA hasn't been "adjusted"
by some moron for adjustment can break it. The trade off is between
power and exhaust smoke, a delicate balance that's achieved on a bench
at the factory - not in someone's back yard.