I know this will not help you now, the damage is done, but for future information, when welding on crank cases or covers it is best to assemble as much of the motor guts (cams Crank, oil pumps and cam cover etc) as possible,
as the internals act as a heat sink and disepate the heat and having the cases bolted together will stop warpage, plus pre heating slowly in an oven,
a few years ago, I built a 45 Magnum where there is a LOT of welding to be done, firstly on the barrel base stud holes for repositioning for the Sportster cylinder bolt patten, and welding the right side of the deck also for the cylinder's to fit and had to weld on welds to build it up close to about a 1/2 inch before machining back to where it needed to be, I did the welding slowly, one bit at a time, bit by bit over 2 days so as not to over heat the cases,
when finished and disassembled prior to vapor blasting and final rebuild, there was no warpage whatsoever,