As you have not placed constraints on the project implementation, consider that most welding requires a jig of some form to maintain alignment of parts. The use of the generality "most" also refers to simple clamping of two pieces prior to welding, which is common in non-critical alignment projects.
Allowing for the specifications you've provided, consider to use a piece of square tubing of the same dimensions as that portion to which the ears have been added. This piece of square tubing would have a hole drilled to match those of the ears.
A bolt of the proper diameter would pass through the holes and through the jigged up square tubing, to maintain alignment and provide a stable structure for welding. If it is not going to negatively impact the primary part, a pair of tack welds to hold the square tube to the main part would provide additional stability.
After the ears have been welded in place, the bolt should be removed and the tack welds ground clear, allowing for the desired pin placement without complications.