Poor acceleration II

I'm starting this new thread on a continuing problem since
the old one has been going for many months w/out resolution and the thread is
getting a bit unwieldy.

THE CAR:  1999 Legacy wagon 2.2L automatic, very nice inside and out.

THE HISTORY:  PO removed the oil drain plug and purposely burned up the
engine.  A replacement engine (same vintage 2.2 phase II) was dropped in with about 140K miles on it.

THE PROBLEM:  very sluggish to (sometimes) non-existent acceleration below 2500 RPM under load (fine above 2500 RPM - this switch spot can vary), intermittent problem, but for
example has been doing it constantly the last two days.

WHAT WE KNOW/DIAGNOSIS: 
If one disconnects the battery and resets the ECU it drives beautifully
for 15-20 minutes then starts to malfunction (did at least 3 times) - I assume
that for these 15-20 min. it is on default settings and then the ECU changes
things and it runs poorly.  Thus it "may" be either a bad sensor feeding bad info to ECU or a faulty
ECU.  IS THIS A VALID CONCLUSION?

Throws no codes unless I mess with the sensor (unplug, check
voltage etc).

THINGS CHANGED REGARDLESS OF ABOVE DIAGNOSIS:

-Spark plugs checked, new and gapped correctly

-new ignition wires installed

-new PCV valve installed

-new air cleaner element installed

-checked for vacuum leaks (fine water spray, engine running)

-checked coil pack for leaks (fine water spray in dark,
engine running)

-checked all engine harness plugs and other secure

 

THINGS CHECKED ASSUMING ABOVE DIAGNOSIS: sensors checked
either by, 1. replacement, 2. voltage input and output. or 3. disconnecting and
see if runs better.

MAF sensor (cleaned, unplugged didn't run), TPS (voltage ok and replaced temporarily), Knock sensor (replaced twice), Pressure sensor (voltage ok and unplugged ran the same), coolant Temp sensor (replaced), front O2 sensor (unplugged it ran the same)

Rear O2 sensor, cam sensor and crank sensor not checked, assume it wouldn't run w/out the latter two.

ANY MORE IDEAS?  Any more sensors to check?

Are there (non-engine) things that one might expect burning
up the engine would damage?  The end of the tail pipe is very black, but doesn't use oil w/new engine.

Should I take it somewhere for a professional diagnosis or
try a $50 salvage yard ECU, or a $250 rebuilt ECU?