Ford Explorer Sport Trac, P0340 P1309 after recent engine repairs?

My 2001 Sport Trac had major engine repairs two months ago, during which all the timing chains, valve springs and valve lifters were replaced. It has run well since then (at least 1000 miles or more).

Now the vehicle is running rough and near-stalling, especially at low speeds. The check engine light is on with codes P0340 and P1309 (pending).

Is it likely that the new problems are related to the recent repairs?

Added (1). The original shop is in a different state, so there's no possibility of taking it back.

I'm not really concerned with assigning blame to the original mechanic; just ensuring that the work that he performed won't have to be redone. If the problem is most likely the camshaft position sensor or wiring, I can deal with it. However, if a timing chain failure is causing the problem, that's a bigger issue. So the real question is, could the new problems be caused by a timing chain malfunction?

The P0340 code indicates a fault with the camshaft position sensor.

That could be a sensor fault or a bad connection, either dirty or not seated fully home - worth checking as it will have been disconnected to do the engine work.

Also look for any wires that could be not clipped properly and chafing or touching something hot, so getting shorted.

The sensor possibly looks something like this, depending on the exact engine:

The P1309 code is a side-effect of that fault.

More info:
https://www.autocodes.com/p0340_ford.html

While it's possible that during the repairs the Camshaft Position sensor wiring/connector may have been damaged or the syncronizer assembly was worn/damaged/not checked and is now having issues which trips the P0340/P1309 codes. It could also just be due to age that the sensor is going bad or has a bad/loose connector, etc… And trips both codes. Did the shop check for damage/wear to the synchro? The synchronizer is basically like the bottom part of a distributor which aligns with the cam and sensor and may have internal damage which can cause issues.

The shop that did the work or another qualified shop if you don't trust them can run some tests of the sensor/wiring or PCM data or inspect the synchro to pinpoint the issue. The P1309 code gets tripped if there's a Cam position sensor or syncro issue but could also be due to a faulty PCM although rare. More likely it's related to the previous repairs or sensor/synchro issue.

Identify the issues and repair as needed, clear codes and test drive to see if any codes come back up.

Synchro repairs…

"What causes the P0340 code?

A camshaft position sensor circuit wiring that is broken, shorted, or corroded
A camshaft position sensor circuit connector that is broken, shorted, or corroded
A faulty camshaft position sensor
A failed crankshaft position sensor
A faulty PCM
What are the symptoms of the P0340 code?

The Check Engine Light will come on
The vehicle may not start, or may be difficult to start
The vehicle may idle rough or stall
The vehicle may misfire
There may be a loss of power while driving
How does a mechanic diagnose the P0340 code?

Uses an OBD-II scanner to retrieve all of the trouble codes that have been stored by the PCM

Inspects the camshaft position sensor wiring for wires that are broken, corroded, or shorted

Inspects the camshaft position sensor connector for connectors that have broken or corroded

Inspects the camshaft position sensor circuit wiring for wires that are broken, corroded, or shorted

Checks the continuity of the camshaft position sensor circuitry

Completes any necessary repairs for other related trouble codes that have been stored by the PCM

Uses a scan tool or oscilloscope to check the camshaft position sensor voltage readings

If the voltage readings are abnormal, the camshaft position sensor will need to be replaced.

If the voltage readings for the camshaft position sensor voltage readings are normal, it is possible that there's a problem with the PCM which may require replacing or reprogramming.

Common mistakes when diagnosing the P0340 code

Before replacing the camshaft position sensor, it is important to inspect the wiring and connectors to rule them out as the cause of the problem. This is the most common mistake when diagnosing the P0340 trouble code.

Another mistake that is made during the diagnostic procedure is neglecting to consider a misfiring problem or a crankshaft sensor problem as possible sources of the P0340 trouble code."
https://www.yourmechanic.com/article/p0340-obd-ii-trouble-code-camshaft-position-sensor-circuit-malfunction-by-jamahl-walker

P1309
"Possible causes

Faulty Camshaft Position Sensor
Synchronize Assembly not properly installed.
Verify the cam sensor is synchronized
Faulty Powertrain Control Module (PCM)
Verify input sensor parameters are correct

What does this mean?
Tech notes
Replacing the Camshaft Position Sensor (CMP) usually takes care of the problem, but if the sensor is installed out of synchronization it will produce the P1309 code. If the CMP is installed properly, REPLACE Powertrain Control Module (PCM). RESTORE vehicle. RERUN Quick Test.

Read more: https://www.autocodes.com/p1309_ford.html

Yes, those codes are for the camshaft position sensors. These would have been worked on when you had the timing chains replaced.