Hinges and bonnets often have alignment holes drilled (as here below) so in theory pins can be used when refitting to get close to the final position. But as I found before taking Bee's bonnet off they were not in line, for whatever reason. This picture also shows how the bonnet holes are slotted vertically, and the hinge holes horizontally, to give loads of scope for alignment.
At this stage the bonnet should be lowered carefully to check the gaps all the way round, especially if your hinges and bonnet don't have alignment holes drilled, or they are in the wrong places. If the bolts are nipped-up just the right amount you can raise and lower the bonnet carefully without them slipping, and when near closed can grasp the bonnet and pull/push it back and fore, the front side to side, and the hinge end up and down, to get the final position before fully tightening the bolts.
Going by the Parts Catalogue the upper half of the telescopic prop should fit against the outer face of the bonnet bracket (and the inner face of the wing bracket) not the inner to prevent chafing, but to do that it needs a special spacer. More info on that here.