I already have 3.9.8 working but i just tried myself with a new blank folder. Live EFT updated to latest and I get stuck using the installer on the step "downloading patcher". Stops at some point here every time. Tried maybe 10 times and could not get it to progress past this point. No clue what is wrong but it clearly is having issues.
EDIT: I tried again and this time it worked for me and it completed successfully. Maybe try deleting the spt-installer cache. I did and it completed after i did this. Type %appdata% into your windows search bar and then delete the spt-installer folder in here and then try running the installer again.
When you say trying to update, what version of SPT are you updating from? If you already have 3.9.x working you do not use the installer. This is for new installs only. To upgrade from a previous 3.9.x version simply download the SPT 3.9.8 7zip and extract it to your SPT install and overwrite all files.