Things got glitchy while trying to find the source of the lag
After isolating individual assets and running tests I was able to figure out the problem was on the main character model. At first I thought it was an issue with the model itself but I was curious about this as it would not lag when the game was initially run.
Apparently similar people have had problems with any asset that had the particle renderer component after the Unity 5.3 upgrade, so after removing this the lag problem was fixed.
Boma's CGA Sketchbook 