After running for a few minutes I start to get checksum errors and read/write errors on the drive.
Do you say you get checksum errors by just *reading* from the CF card (running programs, starting games and so on) or do you do heavy copy operations after you put the card into the Amiga?
And it only starts after a certain time? Such as you run program A and it works ok and a few minutes later you run program A again and it fails to load?
Are there certain actions which trigger the errors?
If after the first boot you leave the Amiga running for a few minutes and only then start testing, do the errors appear immediately? (which might indicate a heat issue)
Did you set MaxTransfer to a good value for all partitions (0x1fe00 is a good value for example).
