Brent. Charlie and Lord Mr. Ford are both giving you good information.
The mid-year 1959 change in FoMoCo y-block engine production was significant. The engineers decided that the length of crankshaft main cap bolts needed to be increased. B9AE, C1AE, and C2AE engine blocks have the benefit of the longer main cap bolts that you want to use.
As Charlie suggested, earlier y-blocks are okay to use, but consider modifying the depth of the main cap bolt holes per John Mummert's recommendation and information. Click the link below for JM's web site info on how to accomplish the main cap bolt hole depth modifications:http://www.ford-y-block.com/ARPmaininstall.htm
Regarding engine rebuilds whether they be dead stock or modified, seriously consider having the complete engine rotating assembly balanced. FoMoCo original factory y-block production balancing work can likely be improved upon. IF you have used replacement parts like pistons or connecting rods, the original assembly balance has likely been compromised. Balancing the assembly will insure smoother engine operation and longer operating life.
Hope this helps!
a.k.a. Charlie Brown
near Syracuse, New York