With cudaminer I am getting a reject rate as high as 25%, anyway I could fix this? For an ati card what would be a good miner to use for clevermining? What kind of rate could I expect to get for a ati card that costs around $350?
Let it run for a longer period, e.g. 12-24 hours and see if the reject rate improves.
For $350 it would be R9 290 that gets maybe 0.9-1.0 MH/s in Scrypt. Depending on your electricity cost it might be unprofitable though. Look into alternative algorithms (X11, X13, etc) for GPUs.
Edit: Overlooked the software question. sgminer 4.1 is probably a good place to start with AMD.