If your original acquisition is HDV and H.264 the Apple Pro Res 422 is fine, you wont gain anything going with HQ or 4444.
Your H.264 files got much larger because H.264 is heavily compressed and not designed for editing, it is a 'distribution' codec. It is best to convert to a I-frame codec such as Apple Pro Res for editing.
Your next problem may be mixing two different frame rates. The Canon 5D records at 30.0 frames per second and the A1 records at 29.97. I use Cinema Tools to conform (slo-mo) my 5d clips to a friendly frame rate. You need to realize audio will not stay in sync over long durations with this conform process.