i've install ETO also in win 8.1 and it's a bit tricky
i've no choice coz my laptop won't allow me to install it in win7..shame on new Asus product
Here's my step install on win 8.1 :
1. install CFS3 master to c:\program files\Microsoft combat flight simulator 3 (never install to c:\program files x86\... mine always got problem to this folder)
2. download patch 3.1a and put that file inside c:\program files\Microsoft combat flight simulator 3 and wait, after succesful report than you can press OK)
3. Install ETO 1.0 (just press Y and OK) it will create it's own install target (use it's default)
4. Install ETO 1.20 (same on step 3)
5. Install ETO 1.40 (before install 1.40 please use remove obsolote file first then install)
6. Install ETO 1.40 update fix (same like step 5 also use remove obsolete file first before install update)
After that you will see 2 different folders in C:\program files\Microsoft games\
one is the original master CFS3 and the other is ETO folder
i use my own way and i just copy all files inside ETO folder to CFS3 master and overwrite anything inside CFS3 master, so there's no more CFS3 master
After that try to run it but before that first make a CFS3 shortcut and choose compatibility in Windows xp SP3 and pick Administrator (mine using this way because im using my Asus laptop so that my CFS3 will running on my GT745m card and not using my Intel HD4000 and also this step you will not encounter any crash or file overide notice, in my game setup it still detect using intel HD but actually it's not )
right now i've 2 ETO in different folder ( 1 for experiment and 1 for backup)
if you gonna make in 2 different folder ETO
first copy all files inside ETO folder to the master CFS3 and overwrite anything insde CFS3 master
then move CFS3 master outside C:\Program Files to C:\ (mine use C:\microsoft games\ETO)
but you have to choose file ETOeraswapper and run CFS3 from shortcut (never use Masterstartup) everytime you change the era or you will lost the mission file sometimes and mission not load
then you install that CFS3 master back to c:\program files\Microsoft games\combat flight simulator 3 and use the same way like step 1 - 6
sorry my step is a bit strange but it's work for my laptop

hope this can help you