" if the smoke unit is used and you have the fan "exhausting" people have reported it pulls the smoke into the loco, not out the stack."
Yes, that would change the exterior effects if the direction can effect smoke generation, second hand.
More likely points to not enough inlet air surface area. Proper/balanced airflow requires equal in and out.
But in case of cooling with little heat added by fan, as long as inflow and outflow effective area are balanced direction doe not matter.
That said, fan direction can be affected by the "order" in which the airflow crosses the electronics.
Typically you want the air to first encounter the non_power electronics to maximize their cooling and then cross over higher power components (think power supply) as you want the higher power components downstream. Spent of number of years in small military companies designing for harsh environments.

Direction doesn't matter. What matters is that there exists another "opening" for the air to intake(fan exhausting) or exhaust (fan intake). Electronics don't care whether air flow is left to right, right to left, etc. It just has to be flowing otherwise you're simply trying to pressurize or de-pressurize the inside and that's not what a fam is for.

Would the Bachmann Offset coupler G88012 solve this.
https://estore.bachmanntrains.com/index.php?main_page=product_info&products_id=14435
Are they no longer including in the locos?

FYI, a batch of Large 2-6-0 parts just became available

Until July 19th, you can use promo code USA250 to take advantage of 25% off your entire order placed through the Bachmann Web Store or Parts Store and receive Free Shipping on orders of $50 or more!

When I Google, I get: 2-4-2T Steam Locomotive - Bachmann Trains 91197
Not 4-6-0.
The OP may have to gives more details on his loco.

PCB06 has the smoker power after the PTC so one must assume Bachmann has taken all into account when they sized PTC. Unless of course they have also changed their smoker.

The grain of wheat bulb (incandescent) does not require a resistor and may be wired direct to track or motor.
The smoker may also be wired directly to track or motor.
I recommend tapping into the motor wires as that takes advantage of the protection PTC on PCB06.

So the chassis (90037 and 90040) available at the parts store are Version 5B
As you noted there are "connectorized" (you don't want to use the phrase plug 'n play)
You only need two (2) connections between your old "shell" and the new "chassis"
They are Headlight and Smoker (if your old shell has a NMRA/Large direction switch, this goes unused, unless you really want to do some major rewiring)
Couple challenges.
(a) The PCB06 in the new chassis is designed for an LED headlight, using it with a grain-of-wheat bulb will probably give little to no illumination.
  There is an LED available on the parts website: https://estore.bachmanntrains.com/index.php?main_page=product_info&cPath=69_139&products_id=4852 and
  that requires some remodeling of the headlight assembly.
(b) To connect the headlight and smoker to PCB06 you would have to add JST connectors that use crimp style pins and you would have to invest in the plastic
  plug housings, the crimp pins, and the crimp tool. Another approach, if you are good with electronics soldering, is to remove the two connectors from PCB06
  and solder wires from shell directly to PCB06. This also requires some skill most don't have.

Yes, the only tricky part is that since the CHUFF TRIGGER is driven by an opto-coupler instead of a mechanical switch, now polarity matters. George Schreyer showed schematics for both the original and the newer chuff sound boards in the Standard 4-6-0 tender. With the newer version, the CHUFF TRIGGER is switching the + terminal of the battery to the sound circuit (essentially powering on and off). Since polarity now matters, the B+ terminal (CON6 pin 1) must be connected to the battery + terminal of the tender. So some wire tracing/ohmmeter work may be in order.

The newer version of the tender chuff sound board is the one with the volume control/on-off sw and was introduced around 2000. Not completely sure how well this new CHUFF TRIGGER signal with work with original chuff sound boards.

Here is the reverse engineered schematic for PCB06.
You cannot view this attachment.

From what I see, you can't get a Gen 7 chassis from the parts store. The only choice now is a Gen 5B.  Something must have happened to the original Gen 7 chassis (i.e. drop/break) and owner had to adopt the Gen 5B or earlier Gen 5. If the pilot truck is a drawbar its Gen 5B, if its a pivoting truck its Gen 5.   Just noticed it has chuff drum so its a Gen 5 chassis.

Mainly from looking at photos on Bachmann parts website.
Starting with this video on Youtube (A Brief Look at the Improved Bachmann G Scale 4-6-0 Front) by RkyGriz.
If you watch carefully you can see that in the new drawbar truck, the axles of the pilot wheels are clearly visible from above.
In the old pivoting truck, the axles are covered by the plastic truck's frame. So you don't see axles from above.
Now go to Bachmann parts store and look at pictures of 90037 and 90040 assemblies.
You can see the axles from above on the pilot trucks, suggesting drawbar pilot truck.
Another data point is the Underframe at the parts store, it has the pivot point structure.
Looks to me like all the older V5 and below chassis, underframes, pilot trucks are sold out and gone for good......
Drawbar Pilot Truck
    https://estore.bachmanntrains.com/index.php?main_page=product_info&cPath=69_671_148&products_id=8545
Newer Underframe
    https://estore.bachmanntrains.com/index.php?main_page=product_info&cPath=69_671_148&products_id=14592

Bill, I think your ID "chart" is great, but it relies on almost all mechanical and physical descriptions (i.e. humps and plugs). As electronics has entered both the Annie and Standard lines, its worthwhile to add descriptive features about the electronics and capabilities.  Like the Standard V5B (if 90037/40 are V5B) now contains a PCB that supports only a limited set of features (i.e. no rear tender headlight) and different implementations (i.e. optical chuff sensor vs. older "drum" sensor)
Just my observations as I wasn't sure what constituted a V5B and when/why it came about.

In reviewing chassis ID sticky and looking at "Standard" (not Anniversary) chassis for sale in parts dept.
Is Loco Chassis (90037) and (90040) (Large 4-6-0 Standard) what is being considered as Version 5B?
If so, description for V5B might be enhanced
  Standard Chassis (not Anniversary)
  Connectorized Wiring
  Main PCB (PCB06)
  Optical Chuff Sensor (PCB08)
  Drawbar Pilot Truck
  Plastic Side rods and detail parts
  Smoke Switch (based on what main PCB06 supports)
  LED headlight (based on what main PCB06 supports)
  No Tender Backup LED (based on what main PCB06 supports)

https://estore.bachmanntrains.com/index.php?main_page=product_info&cPath=69_671_669&products_id=4094
https://estore.bachmanntrains.com/index.php?main_page=product_info&cPath=69_671_669&products_id=12182

These seem to be the only chassis available in the "Standard" line and will require a fair amount of rework (especially soldering)
to rework a V5 thru V2 "Standard" loco.

The chuff drum OR chuff sensor will be on the front driver. Should have one or the other.

The bottom cover (known as Loco Underframe (Large 4-6-0), 900XX-UF-01) contains two long brass strips, left and right that contact the front and rear drivers (the middle is a dummy driver). On a fully assembled underframe (V5B but not V5), the pilot truck wires connect to the brass pickups and then a single pair of wires (track power) go up an into the "chassis".

Underframe
  https://estore.bachmanntrains.com/index.php?main_page=product_info&cPath=69_671_148&products_id=14592
Brass Pickups (Contacts/Pair Anniversary(Large 4-6-0), G812X-MT010
  https://estore.bachmanntrains.com/index.php?main_page=product_info&cPath=69_671_148&products_id=8854