With the bolts of different length: on my bikes the bolts that hold the callipers together are 60mm long, those that hold the callipers to the fork only 40mm. The ones in the kits that I've purchased are 60mm. Both are M10 allen key head. I'm hoping that you haven't assembled the callipers with the calliper mounting bolts.
My three LSs all have Brembo brakes. The 1983 bikes have 10mm mounting holes on the left calliper, but 12mm on the right. There is a top hat spacer/shim on the right to allow use of the same M10 bolts as are used on the left. The "brim" of the top hat is installed between the calliper and the fork boss so it moves the calliper out a bit.
The 1984 bike has 12mm holes on both callipers and top hat spacers fitted both sides.
I strongly suspect that BMW assembled these bikes from the spare parts bin, ATE callipers one day, Brembo 10mm the next, Brembo 12mm the day after that.