I was in the Church for the three days and I attended the English sermon on Friday and the consecration of the Altar and Icons on Sunday. It was a true blessing and it shows his enourmous popularity of H.H. among the Church congregation.
As for the liturgy in the presence of the Pope, there are hymns and responses added to the liturgy, but sometimes the Pope chooses to omit them because they can extend the liturgy significantly. The Pope is most of the time welcomed with "Eflogemenous" hymn that is chanted on Palm Sunday, and the deacons and priests and bishops and metropolitans go outside the church to receive the Pope in two lines.
I asked this question on another forum to prepare for the Pope's visit, and I got this reply from a dedicated deacon in the Copitc Church:
There are a host of hymns and replies specific to the presence of the Patriarch.
Probably the most elaborate is "Kalwc" which is a hymn welcoming the Pope from a safe journey. The hymn has components said in many different tunes such as
and the festal gospel reply.
There is also a selection of hymns which can be said after the Coptic Pauline epistle such as:
Senouda tou makariw
and the hymn of the twelve virtues,
There are also additional doxologies, verses of the cymbals verses, Praxis response, Psalm response, and a selection of altar responses.
Having listed these it is fair to say that most churches will opt not to say these hymns given the time restrictions. It is also safe to say that H.H. will probably cut short any well meaning deacons who chant one of the longer replies or hymns.
Many congregations will probably opt for one hymn and may chant a selection of other hymns at times where time is not a factor such as when waiting for the pope to arrive or other opporunities where there is some "dead time".
I would also be interested in reading what other congregations are planning whether similar or contrary to this.