Is the auto diff campanion flange different from the 5speed campanion flange? Doing the tranny swap and I came across that they may differ and may require the flange to be drilled in order to use the 5speed driveshaft... is this true?

 

the auto and 5 speed use different companion flanges. a new flange is about $100.00. if you pull the flange off, then the differential will need to be set up again. you should also install a new crush sleeve, which requires a torque setting within a specific range to crush it to spec (torque main nut on input shaft / companion flange. this preloads the gears and bearings which also is a torque value. good idea to change the drive shaft seals, and pinion/companion flange seal, check wear pattern/lash on gears.

if you drill holes, and they are off, could cause vibration and weaken the part, if holes are too big then considering the amount of power the car generates, they could elongate and bring on problems due to sloppy fit. then there is the issue of the slight difference in shaft length.
do it right and reduce the chance of creating more problems for yourself. have fun.
chuck