May I suggest, if you have not already done so, attach a 1x1 strip across the channel after inserting the deadeyes and before you attach the shrouds to them. This will keep them from inadvertently/accidentally popping out when you don't want them to pop out.
According to Longridge, pages 166, 190 and193, there should be four eye bolts under each cap, two in each corner at the end through which the top masts (2nd mast section) fit and are at the a 45 degree angle. Two more eye bolts are placed in the middle of the cap, parallel to the sort sides of the cap. This is the same for the main and mizzen masts. The only difference being the dimensions of the caps themselves and the sizes of the cut outs. These eye bolts are for attaching blocks for running rigging. I hope this helps.... I found Mamoli's instructions to be a bit confusing at times. Having a E - I translation helped. I got through it but it would have been nice to have Mr. Longridge for company while I was building my version. You are doing well and getting the hang of it.