I agree with bret about pulling eng,in addition I would NOT use loctite on bolts as from what you say it appears bolts go into tapped/blind holes in oil pan,if you use loctite on bolts & they break again you're going to have a heck of a job removing them from block,a better way is use a flat washer & lockwasher under bolt head.
Pulling eng may also work to your advantage as to possibe cause of bolts breaking as I can think of 3 possible reasons in addition to possible vibration from mower deck.
1-orig/replacement bolts were a little too long & needed a flat washer or two on each bolt & bolt was bottoming out in hole before bolt fully tight against chassis.
2-oil pan casting slightly warped & requires shimming at each mounting bolt.
3-warped chassis,at the factory chassis pan is probably stamped out of one piece of sheetmetal,this can be done in a press with a one shot die,progressive die,automated stamping machine or done in 2-4 operations in seperate presses/dies,I don't know how mtd does it.Looking at assembly drawing/parts list for tractor there appears to be a large clearance hole in chassis pan so eng can be installed/removed with drive pulley installed on eng,if setup man/press operator was a little sloppy in setting up die in press or punches in die were dull/needed replacement when the die opened after punching pan the metal may pull slightly as die opens & punches retract into die,this can cause pan to dome,cup or twist slightly,you might want to use a straight edge & go diagionally across pulley clearance hole & eng mounting bolt holes & check flatness of chassis pan,you might have to use shim stock/washers to level eng on chassis pan.