Hi, thanks. I actually got some help from @muldjord to fix this issue. I'll try to find the thread and link it to here.
[edit]
Here it is. I managed to scrape almost all my troublesome roms using the method @mitu and @muldjord show in this thread.
https://retropie.org.uk/forum/topic/26743/skyscraper-mimic-built-in-scraper-settings-possible/10
I don't use mu .LHA files uncompressed as that is the format WHDLoad uses them in. I only use .CUE when I need CD gamers with the audio.