First of all, congratulation for your recent trip, that is was makes RE owner stands out from others.
Regarding wobbling, in your case there could be various reason but here I think as you had flat tyre, it could be something like imbalanced tyre due to improper fiting as we see in cars, sometimes while getting flat tyre repaired, there is issue of tube not properly settled at center (mechanic calls it "Center out" problem) . Also the level of wobbling you mentioned strengthen the fact that its not properly settled tube inside the tyre.
You may take out all air from tyre and refill if after tapping tyre firmly at all various places and see if it helps.
Beside, you suspect it could be swing arm at fault, we you can test it yourself, when on center stand, check if rear wheel is firm or by checking it yourself.