I'd say you had a pretty good chance in the Mortuary. The strategy to use with Ammochain is to phase immediately at the start. The goal here is to get to either the left or right edges of the map. Use a homing phase device if you got it, but if not normal phases and some luck should work as well. From there pick a row in the center ( I tend to choose the row that you entered from ), and just start throwing plasma down it. All of the enemies should be huddled around the middle, including the Arch-viles. Since you do have the sniper mod pack on your weapon, you'll pretty much kill anything before they even get close to you because you'll always hit enemies in your line of fire, even if you can't see them. Just watch out for any stragglers roaming around searching for items. And if the enemies do get revived, they have to wait a few turns to be able to move, which's more than enough to just gun them down again. You'll know when you down an Arch-Vile if you gain experience, since everything else in the map is revived. This method is the safest way that I know how to do it, except for an invulnerability and nuke. Completing the Mortuary would've also given you another nuke to use.
For the Lava Pits, did you happen to get an invulnerability globe right before it? You could've just nuked the level at the beginning to get rid of the first wave. The Lava Elemental will still spawn and you can kill it with gunfire to get the lava elemental. You might have to do some lava walking to get it though, so bringing some decent boots ( gothic boots if they generated ) is a good idea.
The Shambler isn't that bad of a boss for a rapid fire build. If the missile launcher was available to you, you could've quickly shot rockets to the left right after pulling the lever. The Shambler would've had less of a chance to teleport away since you don't have to reload after every shot, and you could've killed him even before it got a teleport off. If have to fight it though, it might be a problem if you only have shrapnel damage to use against it. In my experience, the Shambler could just teleport away and heal up because its armor reduces quite a bit of damage. You can find a plasma rifle in the lower right room though, and that makes a direct confrontation much easier.
There's one thing that seems odd, why wasn't your equipment a bit more modded? With Whizkid(2), it opened up to 5 slots on weapons and 3 slots on armor, but most of your equipment weren't modded past 2. Did you just lack mods throughout the run?
I did a pretty similar run a few days ago, was actually my first time getting ammochain and using a sniper weapon mod on a plasma rifle:
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DoomRL (v.0.9.9.3) roguelike post-mortem character dump
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Missileboater, level 12 Arch-Vile Lt. Colonel, defeated the Cyberdemon
on level 25 of the Phobos base.
He survived 171075 turns and scored 119474 points.
He played for 1 hour, 36 minutes and 32 seconds.
He didn't like it too rough.
He killed 585 out of 585 hellspawn. (100%)
This ass-kicking marine killed all of them!
He saved himself once.
-- Special levels --------------------------------------------
Levels generated : 9
Levels visited : 8
Levels completed : 8
-- Awards ----------------------------------------------------
Medal of Prejudice
UAC Star (silver cluster)
Aurora Medallion
Untouchable Badge
Grim Reaper's Badge
Angelic Badge
Hell Champion Medal
Hell Arena Key
Hell Armorer Badge
Shambler's Head
Technician Platinum Badge
-- Graveyard -------------------------------------------------
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.................###..........X............................
...........###...###..........................###..........
...........###................................#>#.....###..
...........###.............###......}.........###.....###..
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-- Statistics ------------------------------------------------
Health 46/50 Experience 66166/12
ToHit Ranged +0 ToHit Melee +0 ToDmg Ranged +3 ToDmg Melee +3
-- Traits ----------------------------------------------------
Finesse (Level 2)
Son of a bitch (Level 3)
Reloader (Level 2)
Juggler (Level 1)
Whizkid (Level 1)
Triggerhappy (Level 2)
Ammochain (Level 1)
Rel->Rel->SoB->SoB->TH->TH->MAc->Fin->Fin->WK->Jug->SoB->
-- Equipment -------------------------------------------------
[a] [ Armor ] Angelic Armor [7/7] (96%)
[b] [ Weapon ] modified plasma rifle (1d8)x6 [40/40] (P1S1T1)
[c] [ Boots ] tactical boots [1/1] (100%)
[d] [ Prepared ] modified BFG 9000 (10d8) [220/220] (B3)
-- Inventory -------------------------------------------------
[a] storm bolter pistol (1d9)x6 [30/30]
[b] super shotgun (9d4)x3 [2/2]
[c] missile launcher (6d6) [4/4]
[d] nuclear BFG 9000 (8d8) [40/40]
[e] Railgun (8d8) [39/40]
[f] modified red armor [6/6] (100%) (AP)
[g] modified phaseshift armor [2/2] (100%) (A)
[h] Necroarmor [6/6] (100%)
[i] shotgun shell (x70)
[j] rocket (x14)
[k] large med-pack
[l] large med-pack
[m] large med-pack
[n] large med-pack
[o] large med-pack
[p] large med-pack
[q] phase device
[r] phase device
[s] phase device
[t] envirosuit pack
[u] envirosuit pack
[v] lava element
-- Kills -----------------------------------------------------
90 former humans
77 former sergeants
25 former captains
78 imps
70 demons
87 lost souls
37 cacodemons
27 barons of hell
1 Cyberdemon
28 hell knights
15 arachnotrons
8 former commandos
3 pain elementals
12 arch-viles
7 mancubi
15 revenants
2 bruiser brothers
1 shambler
1 lava elemental
1 Arena Master
-- History ---------------------------------------------------
He started his journey on the surface of Phobos.
On level 3 he entered Hell's Arena.
He left the Arena as a champion!
On level 5 he stormed the Chained Court.
On level 5 he found the Arena Master's Staff!
He defeated the Hell Arena Master!
On level 7 he witnessed the Wall.
He massacred the evil behind the Wall!
On level 9 he entered Hell's Armory.
On level 9 he assembled a tactical boots!
He destroyed the evil within and reaped the rewards!
On level 14 he ventured into the Halls of Carnage.
On level 15 he encountered the Phobos Hellgate.
On level 17 he found the Railgun!
On level 19 he entered the Vaults.
On level 19 he found the Necroarmor!
He cracked the Vaults and cleared them out!
On level 20 he assembled a storm bolter pistol!
On level 22 he was foolish enough to enter the Mortuary!
On level 22 he found the Angelic Armor!
He managed to clear the Mortuary from evil!
On level 23 he entered the Lava Pits.
He managed to clear the Lava Pits completely!
Then at last he found Phobos Arena!
On level 25 he finally defeated the Cyberdemon.
-- Messages --------------------------------------------------
hits the Cyberdemon. The missile hits the Cyberdemon. The Cyberdemon
reloads his rocket launcher.
Fire -- Choose target...
You see : a Cyberdemon (severely wounded) [m]ore | pool of blood
The Cyberdemon fires! You dodge!
Fire -- Choose target...
You see : a Cyberdemon (severely wounded) [m]ore | pool of blood
The missile hits the Cyberdemon. The missile hits the Cyberdemon. The
missile hits the Cyberdemon. The missile hits the Cyberdemon. The
missile hits the Cyberdemon. The missile hits the Cyberdemon. The missile
hits the Cyberdemon. The missile hits the Cyberdemon.
Fire -- Choose target...
You see : a Cyberdemon (almost dead) [m]ore | pool of blood
The missile hits the Cyberdemon. The missile hits the Cyberdemon. The
Cyberdemon dies. You feel relatively safe now. Congratulations!
You defeated the Cyberdemon! Press <Enter>...
-- General ---------------------------------------------------
Before him 198 brave souls have ventured into Phobos:
138 of those were killed.
3 of those were killed by something unknown.
5 didn't read the thermonuclear bomb manual.
And 10 couldn't handle the stress and committed a stupid suicide.
Some rumours though, say that the Cyberdemon was killed already!
Is he immortal? 42 souls claim to have killed him...
4 sacrificed itself for the good of mankind.
37 killed the bastard and survived.
1 showed that it can outsmart hell itself.
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Edit: Small error change