Yep, it's not a big deal to copy the 3.1 files onto the hard drive. Just be careful of any patches you might need for large hard drive support (scsi.device etc.), which 3.9 has but 3.1 doesn't.
Out of interest, is this purely because of not having a graphics card? I have 3.9 on an A1200 running in 32 colours. It's not the greatest looking, but that's to be expected, and IMHO is not that bad considering the 20-year-old graphics chipset. Icons are the correct colours and some dithering of the backdrop allows it to look quite reasonable without stealing all the pens...
