One trick I do for something like a waterpump that has a whole bunch of bolts and many different lengths.
Take the new pump and as you pull each bolt out of the old pump you put it in the matching hole of the new pump. When all the holes are filled you have all the bolts out. No extra bolts hidden under goo. Once the old pump is off, transfer the bolts back into the old pump. Now you have all the bolts perfectly laid out ready to install into the new pump.
I bet you missed a bolt or two.