Praise be to Allaah.
If the deceased had repented to Allaah for not praying and was keen to perform prayers before he died, then there is the hope that he is a shaheed (martyr), because the Prophet (peace and blessings of Allaah be upon him) said: The martyrs are five: the one who dies of the plague, the one who dies of an internal disease, the one who dies by drowning, the one who is crushed by a falling wall and the one who is martyred for the sake of Allaah. Narrated by al-Bukhaari, 2829; Muslim, 1914.
Al-Nawawi (may Allaah have mercy on him) said: The one who dies of an internal disease refers to stomach disease, i.e., diarrhoea. Al-Qaadi said: And it was said that it refers to the one who is afflicted with dropsy and his stomach swells; and it was said it is the one who suffers from a complaint in his stomach; and it was said that it is the one who dies from any kind of internal disease.
From Sharh Muslim.
1 - It is obligatory to pay the zakaah that is owed from past years, by estimating how much he owned - each year - of permissible wealth on which zakaah is due, such as currency and gold, that reached the threshold at which zakaah becomes due and that had been in his possession for a full hijri year, and without including the haraam interest. One quarter of one tenth should be paid on that, i.e. 2.5%. Then what is left for the following year should be estimated and 2.5% paid likewise, and so on.
2 - With regard to what his heirs have consumed of interest (riba), they should repent from that, if they knew that it was haraam, and they should try hard to make du'aa' for their father that he be forgiven by Allaah, because consuming riba is a major sin. May Allaah protect us and all the Muslims from that.
3 - The heirs are not entitled to anything from the certificate mentioned but the original capital. It is not permissible to take the haraam interest. If the bank insists that the heirs take it, it should be taken from the bank and given to the poor and needy, or spent in the interests of the Muslims, so as to get rid of it. See question no. 20695.
If there is an Islamic bank whose transactions are governed by sharee'ah, it is permissible to invest the money through them.
Ongoing charity (sadaqah jaariyah) may be done in many ways, such as building a mosque or contributing to the building, buying books for seekers of Islamic knowledge, buying Mushafs to be placed in the mosque, or donating a house or shop as a waqf and stipulating that its income be spent on the poor, orphans, relatives, students or others, as stated by the founder, or donating money for building a charitable hospital, and so on. In some countries there are organizations that are responsible for waqfs, which you can contact and establish a waqf or contribute to one through them.
The best way in which you can benefit the deceased after his death is to make du'aa' for him and strive hard in making du'aa' for him that Allaah bestow His vast mercy upon him and forgive him his sins.
We ask Allaah to accept (your good deeds) and to help you to honour your father.
And Allaah knows best.