First Scan - advice needed

[texaselite]

Steps I took.

Hooked up ALDL to ElanScan USB (Windows 7), Ignition turned on.

1) Start Talking --> Getting "No Reply" continuously -- checked latency setting and it was set to 1, not sure how to get this to work.
2) I went to SETUP in ElanScan and selected "Test Mode". This time when I pressed Start Talking, it worked!
What is Test Mode and how is it different?
3) Start Logging (still in Test Mode) and took it for a drive around the neighborhood. Unfortunately, couldn't really open it up too much, a lot of stop and go traffic and didn't want to risk getting in a major road and risking engine failure.
4) Saved log (attached).

Background on the car/repairs below, but bottom line right now is I have CEL 41/42 and definitely not running 100%, very inconsistent (runs well for a little bit, but stalls out every once in a while, exhaust pops every once in awhile, etc.) From what I have read, it sounds like it could be any of the following:
Ignition Control module
HES (even though it was replaced 1k miles ago)
Gaps on HES sensors
Timing
Entire CAS (which would also include the magnetic pickup)
Sparkplugs
Leads
Coil Packs
HT lead on coil pack
Earthing on coil pack
ECM

Any advice on next steps?

BACKGROUND
91 Fed, about 40k miles on it now

July 2010 (when it had about 37k miles),
Experienced some mis-firing (no CEL)
-Replaced Ignition Wires
-Coil Packs
-Spark Plugs
-Yokohama S.drives on all 4's
Things OK until...

August 2010, experienced some overheating while driving (fans did not engage)
-Replaced Thermostat (the existing one was definitely stuck according to boiling water test)
Things OK until...

November 2011
Experienced mis-firing again (no CEL) - this time very badly, sounded like a helicopter driving and not all cylinders firing
Also noticed some loose metal chunks in my muffler (disintegrated cat?)
-Purchased Head Gasket Leak Kit -- no signs of HGF
Car basically sat in garage until...

March 2012
Running ok (mis-firing magically gone), but then get CEL Code 41
Garaged until...

December 2012
Car towed to mechanic for a flurry of repairs and upgrades:
-HES replaced
-New timing belt
-Piper stainless 2.25" w/sports cat
-Piper ceramic downpipe
-Wastegate ported to 20mm
-02 sensor
-Oil Cooler replaced/Oil Pan Gasket/Valve Cover Gasket
-ProTech suspension (w/SJS springs)
-Front upper ball joints/Front lower ball joints/Front lower control arms/Various bushings
-Rotors/Brakepads/Stainless hoses/Master Cylinder/Caliper Seal & Sliding Kit
Car runs like a champ, except boost creep when pushed extremely hard until...

July 2013
Less than 1k since the above work, CEL Code 41 and 42 (can HES go bad that quickly!?) and car very jumpy
Garaged for almost a year (frustrated with dumping money in the car) until...

September 2014
Mechanic doesn't really worry about CAS/HES or EST (Code 42)
-Fuel filter replaced
-Thermostat replaced
-Temp Sensor replaced
Car runs much better than it did when I drove it to the mechanic (very jumpy, stalling out), but still have CEL 41/42 and definitely not running 100%, very inconsistent (runs well for a little bit, but stalls out every once in a while, exhaust pops every once in awhile, etc.)

[saska]

Steps I took.
Hooked up ALDL to ElanScan USB (Windows 7), Ignition turned on.
1) Start Talking --> Getting "No Reply" continuously -- checked latency setting and it was set to 1, not sure how to get this to work.

You want the USB Serial Port under Contol Panel > Device Manager > Ports to have the following settings:
bits per sec: 9600
data bits: 8
parity: none
stop bits: 1
flow control: none
In Advanced: you want USB transfer Sizes both 4096
Latency: 1 ms
Timeouts both 0
Serial Converter: Ticked

Only other suggestions I can make are plug the cable in before you start the laptop since things may behave differently whether the laptop uses Std, ACPI or UEFI BIOS and ensure the cable is plugged into a USB 2 port (black) not a USB 3 port (blue). I know they're supposed to be backward compatible but if you believe that, I've a nice bridge to sell you. USB to Serial converters are notoriously problematic.

2) I went to SETUP in ElanScan and selected "Test Mode". This time when I pressed Start Talking, it worked!
What is Test Mode and how is it different?

Dunno

3) Start Logging (still in Test Mode) and took it for a drive around the neighborhood. Unfortunately, couldn't really open it up too much, a lot of stop and go traffic and didn't want to risk getting in a major road and risking engine failure.

That file is garbage -- it has you doing 223 MPH amongst other improbable readings. Suggest you check the port settings as above, reboot with the cable plugged in, plug into ALDL, turn on ignition, F2 to start logging and try again without Test Mode. Don't worry about a few data errors, you may get a good scan anyway.

[Fredjohn]

Disconnect the Elanscan cable, take your laptop into the comfort of your front room, put it into test mode and click start talking then start logging.

You will see it running: that is because it is purely a test cycle working from an inbuilt memory file (I think) and doesn't actually record what your car is doing!

Apart from trying settings as per saska, try changing the com port from 1 to either 2 or 3. Mine works on Vista or Windows 8 on Com port 3.

[texaselite]

I am running Windows 7 Professional and have tried every combo known to man. Tried 3 different drivers, multiple ports, re-installs, etc. and still getting NO REPLY, NO REPLY, NO REPLY...very frustrating.

[saska]

I am running Windows 7 Professional and have tried every combo known to man. Tried 3 different drivers, multiple ports, re-installs, etc. and still getting NO REPLY, NO REPLY, NO REPLY...very frustrating.

Go to Control Panel > Device Manager > Ports > there should be a USB to Serial Port
Are you using the same Com Port number in Elanscan as is listed in Device Manager?

[texaselite]

Yes. Have tried the default port set after driver is installed, changed the port to see if a different one would work, and also tried everything on Windows XP laptop I got my hands on....no luck