Alright, Ubers it is then.
First thing to do is to drop Venusaur and Arcanine from the team. They're honestly gonna be dead weight for you in Ubers (and are terribly outclassed, and being really outclassed in Ubers is something you don't wanna be), and it frees up space to fill a few holes anyway.
But we'll look at the sets for the Pokemon that we are gonna keep before filling those 2 slots. Starting with Jirachi. I think that something like this would be best for your team:
Jirachi @ Leftovers
Ability: Serene Grace
EVs: 248 HP/252 SpD/8 Atk
Careful Nature
-Stealth Rock
-Thunder Wave
-Iron Head
-Fire Punch/Ice Punch
This does a few useful things for you:
It sets up Stealth Rock. Entry hazards are stupidly useful in singles, and Stealth Rock is easily the best of the 3. The damage it provides in invaluable for putting pressure on Rock-weak 'mons and inching threats closer to KO range. Thunder Wave provides a way to cripple Xerneas and Mega Salamence (as well as other fast pokes), 2 HUGE threats in the Ubers meta. You always need at least a little something for those 2. Iron Head gives you something to shred Mega Diancie with and do some damage to Xerneas. Last slot is simply coverage. Fire Punch hits Ferrothorn hard, while Ice Punch hits most of the Dragons a little harder than STAB Iron head will. A specially defensive spread helps you not get OHKO'd by GeoXern.
Next is Primal Kyogre. It's not the king of Ubers anymore like it used to be pre-ORAS, but it's still fairly good. Things is, your current set has 3 Water moves and Calm Mind. As powerful as rain-boosted, base 180 Sp.Attack Water STAB is, having 3 Water attacks as your only attacks is just begging Primal Groudon and bulky Water resists to come in and wall you to hell and back and then some. It needs coverage, something like this:
Kyogre-Primal @ Blue Orb
Ability: Primordial Sea
EVs: 252 SpA/252 Spe/4 Def
Timid Nature
-Origin Pulse/Water Spout
-Thunder
-Ice Beam
-Calm Mind
Nature and EVs let it speed tie with other max Speed base 90s, but you can alternatively run a Modest nature and take some Speed out and place it into HP or something for even more firepower and a little bulk. Thunder allows it to destroy opposing Kyogre and Water Arceus, while Ice Beam threatens all the Ice weak pokes in the tier.
Since you're using Gengar you might as well use it's Ubers-only Mega Evolution:
Gengar-Mega @ Gengarite
Ability: Levitate---->Shadow Tag
EVs: 248 HP/84 SpD/176 Spe
Timid Nature
-Perish Song
-Protect
-Taunt
-Disable/Substitute
You could also keep your current EV spread and useShadow Ball+Focus Blast+Sludge Bomb+Taunt for a more offensive version to kill Latias and Giratina-O, common Primal Groudon switch-ins and general annoyances.
And then there's Arceus. Arceus in general is a top threat since it can be any type and has a pretty good movepool that lets it be somewhat versatile. Some Arceus forms are not so good though. Arceus-Dragon is one of those. In a tier filled with Dragons there are better options for a Dragon type than Arceus (read:almost all of them) so why use Dragon Arceus? A better one for your team would be Ground Arceus imo.
Arceus-Ground @ Earth Plate
EVs: 252 Atk / 4 SpD / 252 Spe
Jolly Nature
-Swords Dance
-Earthquake
-Stone Edge
-Recover/Ice Beam
or
Arceus-Ground @ Earth Plate
EVs: 252 HP/ 4 Def / 252 Spe
Calm Nature
-Calm Mind
-Judgment
-Ice Beam
-Recover/Refresh
Ground Arceus provides you with something to absorb enemy Thunder Waves with and checks Zekrom and more importantly, most Primal Groudon variants. The first set is a straight up attacking set that has a lot of power after a Swords Dance and gets good coverage with EQ+SE alone. Ice Beam probably seems weird on it but it's actually good for sniping Mega Salamence, who often likes to come in thinking that it'll get a set-up opportunity since it is immune to Ground type Judgment and can weaken the inaccurate Stone Edge with Intimidate. But Recover's still good. The 2nd set is a more tanky set that's not burn bait, though most people prefer the first set.
Ok, now we can get to the 2 empty slots. Filling the first one is easy. Ya just gotta put in this motherpsyducker:
Primal Groudon is the current King of Ubers, finally dethroning Kyogre in ORAS after living in fear of it for 3 generations. Desolate Land is a fantastic ability for it, eliminating what would be a crippling weakness for it and boosting its new found Fire STABs. It can check Xerneas to some degree. It has a great stat distribution, sporting crazy good mixed attacking stats and having good natural (physical) bulk. It's versatile as psyduck because it has so many viable options and can legit fit on any team in Ubers.
....Does have a few issues though despite its greatness. Its STABs are walled (unless you Swords Danced) by muk like Latias and Giratina-O/A, it's Sp.Defense and Speed (unless it Rock Polished) leave something to be desired, and it lacks any sort of recovery besides Rest. It also has 4 moveslot syndrome a little bit.
But it's still really good.
I'll let you come up with a set for it though and see what happens. Just remember that it has to hold the Red Orb.
As for the final slot....we can work that out once you've read all this and thought about a Primal Groudon set. Feel free to ask questions too.
