I think the 2.5 billion price tag would include salaries/pensions of the staff of the proposed armed forces.
People are already contesting SNPs figures, saying they are much too optimistic and in reality would cost a lot more.
As to how they can afford it- were they an independent country, they would have their own income stream, being able to raise taxes via individuals and corporations, they would have a share of the oil/gas revenue, all that kind of thing. The question Scots should be asking would be; is that going to be enough to support their current and future infrastructure requirements, especially since revenue from oil and gas reserves are going to dwindle over time.
And at least part of SNPs calculations regarding Independence will have rested upon becoming part of a Sterling zone and becoming an independent member state of the EU - but both of these presumptions have been challenged in recent debates.