The studs will pull the caps a little outa round for two main reasons. The first being the torque values change slightly as the threads on the stud are little better then then the stock bolt. The better fastener usually gets a little more load even though the torque value may be the same. The second, the stud will pull the block slightly different than a bolt. Sometimes its enough you can get away with it and sometimes it's not. It always best to error on the side of caution.
You need to get the pump issue fixed. It doesn't look like you have hurt the bearings with lack of oil yet but it's never good.
Is your block had the main bored or honed? Was the crank installed new or was it checked for round journals?