TLDR; If you give a god multiple favored weapons, how badly is this going to come back to bite you?
Just make users/casters/whatevers pick one of the available weapons in any situation that references a Deity's favoured weapon, and all should be hunky-dory.
Of course, if you want multiple simultaneous favoured weapons, then all bets are off. Clerics are already pretty powerful, they don't need another boost.
They're gods. Give them proficiency in as many weapons as you want. There aren't any rules for how gods are statted because Pathfinder doesn't generally have a bunch of godkilling. So do whatever you feel works best.
Favored weapons should be chosen for what you want clerics to be proficient in.
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I'm going to rain on your parade for a bit. If a cleric wields a heavy shield in one hand and a sword in the other, what is he using to cast his spells? A light shield might work but you'd have to put your sword in to your shield hand every time you want to cast. I think they also need to hold or touch their holy symbols for some spells.
There's the feat bit too, as Coidzor mentioned.
I'm not sure dirt is the best material. Granite, marble, gold or even platinum might be a better choice.
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The only really relevant characteristics of gods is their alignment, their domains and the favored weapon they confer on their followers.
If I were you, I'd model a pantheon on an Earth pantheon that more or less resembles the style of society your game world most closely corresponds to. I mean, I did finally get used to the Forgotten Realms pantheon, then more or less ported over my references to the Pathfinder pantheon, but the more original (and hence unknown) your pantheon is, the harder it will be for players to identify with it.
Just my $0.02 worth.
While Paizo hasn't created the stats for gods yet, they have done so for several demigods. They should give an example of how powerful these entities should be: Cthulhu CR30, Pazuzu CR30, Tarrasque CR25, and Glaistig.
Dreamscarred press did stat some deities in the The Tome of Horrors Complete, to give other examples, such as Orcus CR 35 and Oinodaemon CR 37.
One thing to keep in mind about the favored weapon is that clerics are already proficient in simple weapons. So in the case of spear and shield just make the shield the favored weapon and the deities clerics will be able to use both.
Too really use the spear and shield is pretty feat intensive and requires stats the cleric is unlikely to have. Most spear and shield builds use two weapon fighting which requires a high DEX. The base two weapon fighting requires a 15 DEX. Clerics already need good WIS, CON and CHR if they plan to channel energy. If they are going to be engaged in melee add a good STR to that. Cleric also do not get any bonus feats so will have a difficult time being able to use this style of combat. About the best you would be able to do would be to pick up improved shield bash and use the shield to hit when you need to do blunt damage, or do not have a spear.
A warpriest might be able to pull this off. First of all they already have proficiency in martial weapons. Second they use WIS for all class abilities including channel energy, so are less MAD. And last but certainly not least they do get bonus combat feats. If you really want a combat focused cleric the warpriest is probably a better way to go anyways.
As to stating up the gods, that is something that is actively discouraged by Pathfinder. As several people have mentioned you need very little game stats for a deity. Instead of spending time creating a stat block use the time to work on the background of the deity.
There is a percent for deities with multiple favored weapons—the dragon deities of Golarion usually have a natural weapon and a manufactured weapon.
I would say, keep it to only one favored weapon, not armor or shields. Also I would go with Gods can use any weapon because their Gods, but they stay with their favored weapon.
I made a god, well more like a collection of small house spirits conglomerated into a single god, that had all simple weapons as favoured weapons. Given that clerics already have proficiency in simple weapons, it doesn't make too much difference to have multiple.