Hello,
Normally, the third person singular "s" is one of the last morphemes to be acquired (although it is surely not the last to be learnt!); so I would advise one not to stress too much, for such a thing will work itself out with time

By the way, many a linguist predict that this "s" will disappear in a short time, much like the former English declensions. So maybe we can stop teaching it now.

However, if you wish to try to do something about it, then perhaps you might do a review session. As a boring/fun communicative activity, the students might form groups and construct and conduct a short survey, for example, At what time do you eat dinner? Do you like beer?. Once the questions have been answered, the group members can report their findings to the class, while focusing on the third person "s." For example, "I interviewed José, he eatS dinner at 7:00. He doeS not like beer.
The past tense "-ed" might be something to worry about. Although, in casual speech, the "-ed" tends to be reduced (my observation); it can be damn difficult trying to lump all of those word final consonants together.
Consider doing a review of the past tense and have the students practice the difficult word final consonant clusters. As a communicative activity, perhaps the students might tell the class or a partner about what they did last weekend. They can practice by both speaking and writing their story, while paying special attention to the "-ed."
Good luck!