Here is how I see the situation panning out.
All MoD bases in Scotland will have to be closed down and moved, I'm sure there will be a transfer of Scottish solders but the knock on effect to the economy will be huge. I imagine most of the bases could be transferred to Wales. With purely Scottish regiments remaining.
Devonport Dockyard is the only commercially viable shipyard in the UK, Babcock Marine have been trying to damage that but the others only exist because of the work the MoD gives them. Ever since hearing the size of the defects list on the HMS Ocean (brand new from Scottish Dockyards) and knowing how long that ship had to be refitted to be functional I think very poorly of the Scottish ship yards. Currently the Scottish yards are constructing Type 45 and Astute Submarines. I doubt the Scottish government could afford projects of those size.
If Scotland left the United Kingdom it would lose it's EU status (initially causing exports to become vastly more expensive) while I'm sure an EU trading agreement could be established quite quickly (or during the exit). I don't believe the new independent Scotland would meet EU membership criteria, assuming that it did it would take 5 - 10 years. The UK does benefit with £4-5 billion of investment from the EU. Scotland would no longer get that investment.
You would also have problems with passports, losing it's EU status would mean more restricted movement. You could no longer be in the EU isle when going through customs in France, Germany, etc... Scotland would have to negotiate hundreds of agreements across the world (e.g. extradition and trade), establish Embassy's in its key export markets (more cost).
What about the oil reserves? Without a fleet Scotland (unlike regiments there are no Scottish ships after all) couldn't enforce it's right to territorial waters. So the collecting tax on oil would prove difficult, I wouldn't be surprised if Scotland did leave that the UK tried to maintain rights to those oil fields. you also have drug smuggling/ human trafficking. Without a fleet Scotland becomes a great way to illegally import, either England polices the waters for a cost or England would have to build a giant fence along the border.
I tend to buy Scottish lamb in part to support the UK. If Scotland left the UK I would either buy Irish/Welsh/English lamb or just go for the cheapest (if I'm sending money out of the country I might as well minimise it). How many others do similar things and what would be the affect on Scottish trade?
While I am sure all of these problems could be overcome I strongly doubt the SNP are capable, watching Holyrod in session made me feel a lot better about the competency of Westminster (and I think poorly of Westminster). The SNP like to talk about independence like it will solve all ill's, but unless it occurs over decades I strongly believe it will put Scotland in to a serve recession for a decade. Yes Scotland does well with its budget but once you factor in additional costs (it's own embassy, military, etc..) and the fact it wouldn't have the same bargaining power (losing the NHS) I think things like free prescriptions (possibly even free health care) and free university will have to go and Scotland will be worse for it.
I support every countries right to independence I just can't help but think if Scotland become independent England will be leading the way with emergency relief 10 years after it happens.