I had to file form 8962 but instead of just sending it with my 1095- a I sent the whole amended return in will that effect my refund time?

Hard to say.  I'm not sure where IRS stands right now in processing the 8962/1095-A responses, but an amended return will take at least 8 weeks to process (IRS says up to 16 weeks, but that's on the long side).  Wish I had better news.