I've been making notes for a few years on a monotheistic campaign world I'm building in my copious (ha!) spare time. These are some ways I'm expanding the clerical stronghold rules:
When a cleric reaches 8th level, the place of worship described must be built within the civilized realms of <the main continent> at a location consented upon by the church. This may be an area of expanding population, the re-establishment of a church previously abandoned or ruined, or other reason as defined by the DM. Success in this endeavor gains the character the ecclesiastical title of Bishop.
If the character previously developed a patronage relationship with a noble of the appointed realm, the place of worship must be at minimum 2.5X as large (5000 SF Main Floor) and is expected to be of a greater magnificence as well; ideally, a structure of cultural significance similar to many of the great medieval churches. The patron defrays between 51%-60% of the total cost of the building (overall maximum patron contribution subject to DM discretion).
A place of worship deemed culturally significant by the DM raises the minimum hit points of those worshipers to a floor of 2 hit points, after having dwelt within its diocese for an uninterrupted period of at least 3 years (if they leave they must start the 3 years anew). Any worshiper attending the location a minimum of once a month for an uninterrupted period of months gains a 2% cumulative "miracle" bonus to their chance per month of a cure of any existing chronic diseases and/or parasitic infestation. A culturally significant church will triple the number of pilgrimages made to the location.
Culturally significant buildings also attract 50% more followers to the cleric than otherwise normal; all followers arriving over a period of 12 months. Should a cleric call for a Holy War (see below) as the prelude to building a religious stronghold at 9th level then 2-8 first level paladins - younger sons of lesser nobility or other worthies as determined by the DM - will join to help lead the forces to Holy War on the presumption of forming the core of the new Archbishop's court. (Note: a cleric may call for Holy War regardless of the type of place of worship built at 8th level, but paladins only assemble if it is culturally significant.)
A religious stronghold built at 9th level must be in a location not currently under the titular power of another if the cleric wishes the recognized rights of a Sovereign Archbishop. Unlike the place of worship at 8th level, a location of a religious stronghold is chosen solely by a cleric, although if sovereignty isn't desired the stronghold may be built in another noble's realm as per a place of worship, above, but this does require consent (which is usually welcomed). Religious strongholds built in either the Near or Far Wilderness grant the cleric the right to call for Holy War. This involves expending between 500 - 1,000 gp per month (1d6+4) for a year on messengers, advertising, travel assistance, and other costs as determined by the DM.
Holy War results in the accumulation of the following groups at the previously-built place of worship, or alternate designation advertised by the cleric during the proclamation period: between 100-600 families of farmers and other trades useful in virgin settlements (each family having between 1-6 people); 100-400 untrained men recently gaining their majority; and 100-600 experienced mercenaries seeking long term employment (which do expect pay if retained). Lastly, calling a Holy War means certain availability of at least one prospect (and possibly several) of any specialist hireling type of the cleric's choice that they wish to retain, so long as that type is at least occasionally available generally. In all cases, those assembling expect the cleric can provide for their needs during the journey and afterwards for one year or until the first harvest comes in, whichever occurs first.
While military failure in a Holy War isn't necessarily disgraceful, an inability to provide for prospective settlers during this initial year is. Such prospective archbishops may lose all ecclesiastical titles and suffer permanent reaction penalties that double with the lower classes. If the failure is especially great or neglectful, personal atonement may be required from above.
While a cleric isn't absolutely required to relinquish their bishop title to the previous place of worship if becoming sovereign elsewhere, most appoint a functional under-bishop and retain the title only ceremonially - perhaps a small stipend taken from the church's revenues. The consenting noble may insist upon nominating a replacement to this first title otherwise, unless relations remain friendly or the noble is under church censure. However it is not unknown for such revocations to spur a conflict which can end in a noble's loss of title and rights to the cleric instead; but given the great disparity in resources between the two, and the church's natural desire to intervene in such cases, this outcome is rare.
The farther away an intended new realm is from the civilized lands, the greater the cleric's likelihood of beatification after death (assuming the stronghold was successfully established, in most cases).