Hi Danpatch,
I would agree with nmarman that the the long term injury sounds like it is involving the distal (lower) Achilles tendon, be it an insertional tendinopathy, a lower mid-portion tendinopathy, a retro-calcaneal burstitis or a mixed picture of more than one entity.
Without examining the area in person it would be difficult to differentiate between the potential causes although the description of trouble with putting on shoes would suggest that the bursa could be involved. As the treatment for the different causes will vary your best bet is to go see a good sports physio or sports rehabilitator who will be able to pinpoint the problem and therefore focus any treatment and rehab needed.
As for the anterior (front) pain I would very much disagree with a diagnosis of medial tibial stress syndrome! The pain has only been one day in duration, from your description it is located over the anterior tibio-talar (ankle) joint and given the history of using the over-sized flippers it is most likely a straight forward strain of the anterior joint capsule/anterior tendons which will settle down with some icing and a few days of relative rest (ie avoid using flippers untill it has settled down).
Anyway its the achilles problem that needs more attention as if you have had it for 5 years it is unlikely to go to go away on its own. Bite the bullet and get in to see someone about it, they wont be able to fix it overnight but should be able to give you the exercises you need to manage it yourself and slowly get it under control.
Regards