I think I found the issue with this scenario.
In TOAW III you can/could use custom graphics for each of the many icon counter sheets.
In TOAW IV that is no longer possible, instead you use the default counter sheet and the default colors and then you can customize those colors with an xml file.
The way TOAW IV works now is that it uses the h_unit.png file for the icon's themselves and then you (as the editor) can override that with the colors xml file.
This is why you won't see any 'custom' icon's that are in this (and it's family/group of scenarios). The way to fix this is to make a copy of the h_unit's file and insert into the second slot that MACV in place of the HQ icon that was previously there. The problem with this scenario (and the whole group of the scenarios in this series) is that each of those custom counter sheets may not use a MACV and instead use something else in that slot, so this solution may not work in all cases.
Here is an image showing the issue, on the left is the new TOAW IV h_unit.png file and on the right one of the custom counter sets:
To further illustrate the complexity of this problem with this scenario and how TOAW IV works is that this file: units_1_017_0.png has the text MACV in the Second Icon Slot but in this file: units_1_017_1 uses ATF as text in the First Icon Slot, and this file units_1_017_2 uses the text MAF in the Second Icon Slot. So each file that was customized in TOAW III would have to have a unique icon slot since all of these are global (the h_units.png).
So as long as all the custom TOAW III units_* had unique places for the custom icon then you could create a master h_units.png file with the MACV, ATF, MAF etc. and ship that within the new scenario folder structure to pick it up.