I pulled apart my second hand carbon mast and 95 plus fuselage.

When I went to reassemble it, I noticed that if I set the mast all the way into the fuselage the cross bolts no longer align by about 1mm or so. Are the cross bolts supposed to align when the mast is fully seated? It is possible my mast was sanded down hence the question. In the picture below I have aligned the cross bolts but there is considerable play when I do that. The plastic spacer is good condition, and It is the same with the 115 plus fuselage that I have. If there are supposed to align then it should be a simple fix.

Also many of the SB carbon masts require a plastic shim part from starboard to separate the carbon mast from the al fuselage. I assume that is the plastic spacer you are referring to.

Can't say for sure because SB has many variants the look the same, but are slightly different and not really interchangeable.

Yes, the bolt holes should align.