Took some effort, but seems like the game is working. Installed into a windows vista bottle and performed a maximum installation. Also applied the official 1.02 patch, ff7_opengl-0.7.11b patch, and Laptop_Keypad patch. Applying patches requires running non-Ultima version of the game. I run the game within a 1024 x 768 wine virtual desktop. Installing the ff7_opengl-0.7.11b includes a special ff7_opengl.cfg in which you can also specify to run the game in whatever resolution you want (e.g. 1024 x 768.) Any configuration files should be editied with Text Wrangler to ensure it maintains the Windows Carriage Return (CRLF) characters in the file. Config file also has a setting allowing characters HP/MP to exceed original 9999 limit.
Main problem I still encounter is certain menus do not respond to customized keyboard mappings. I suspect they use keys that are static and cannot be changed. For instance, when I select Quit from the in-game menu, it presents the confirmation window but I cannot find any keys that seem to select anything. After I save I must quit the bottle to exit the game entirely.
I will continue to experiment with the menus, patches and configurations to see if I can figure out some of the menu navigation problems. Once I'm comfortable I have a good process, I'll post to either here or Tips & Tricks.