When I gain bonus MODs from controling a continent, do those MODs have to be placed within the area that provided the bonus, or can they go to any territory I control? No
Yes, that territory becomes 'neutral', as in not controlled by any player.
When a nuke card eliminates the only MOD on a territory, does that territory stop being under the defending players control?
yes, the defender may roll one or two dice as (s)he chooses when he has at least 2 MODs in a territory
During an attack, can the defender only chose to roll 1 die and therefore only lose 1 man per attack, or is he forced to roll 2 if he has 2 or more MODs in the defending territory.
Yes (effectively doubling the value of whole continents)
Im also not quite sure how the game ends. Do you add your continental bonus ontop of the score for territorys controled?
Also, does a frequency jam card played on the last turn prevent a player from playing colony bonus cards to boost his end of game score?No, frequency jam only works during the players turn when it is played. And at game end, all player's turns have already ended.