Hi Regan - glad you liked it when it was working
More than likely what happened was you had a cold or loose joint somewhere which was making a connection when it was boxed up, and now has been 'disturbed' as it were during the disassembly process. When you say 'faint swirling sound' do you mean a swirling in the background white noise through the amp, or a partial signal from your actual guitar playing? The reason I ask, and this is consistent with the scenario you describe - if it's the background white noise, it's one of your offboard connections most likely and you can focus on re-flowing those connections.
If it's a partial guitar signal, that happens to be faintly swirled, it's more likely on board. If so you can start by re-flowing your joints, especially any which look dull or blobby. I was just doing this last night with my own Phase Royal build - and the joints under the pots are a little tricky. You have to bend the PC mounted pots out of the way to get in there.
Best reference on building there is, is Stephen's tips which is stickied at the top of this forum.
Clean inside, dirty outside is how like i like 'em!