Don't be dissapointed w/ the Black Ice being so small... that's its best feature!

The Eheim pump has fittings that can be twisted off (at least the 1250 does). So you can change them. So let me see here...
1. As far as the Black Ice being damaged, if a few fins are bent, you should be fine. Every time I order a radiator there are always a couple fins that are bent. However, that is up to you...
2. It looks like your eheim has 3/8" ID hose fittings, although that seems odd to me. Where did you order it. When you go to a store, you cannot merely specifiy an inch rating. You MUST tell them ID or OD, otherwise they won't know what you ordered.
3. Are you sure the Black Ice has 3/8" fittings you said that they hose "sorta" fits over it. That could be 3/8" hose stretching over a 1/2" fitting... You should try unscrewing the barbs on the pump and going to home depot to grab some new ones. Did you get thsi stuff from the same place?