After discussing assemblies a bit, it seems like a good way to go with a chunk of them (and given what's already in the system) is to upgrade standard weapons into pseudo-exotic ones, possibly uniques depending on the mods involved. Since these can't be modded further, they should be marginally better than their (unmodded) counterparts. For example:
Speedloader Shotgun (combat shotgun + PT, pseudo-assault rifle):
Damage: 8d3
Clip size: 6
Fire time: 1.0s
Reload time: 0.5s (straight loading, no pump)
Accuracy: N/A (combat's spread and drop-off)
Reinforced Plate (red armor + PO, pseudo-gothic armor):
Armor: 10
Durability: infinite
Knockback: -90%
Move speed: -70%
Prophylactic Armor (blue armor + BB, pseudo-medical armor):
Armor: 2
Durability: 200%
Knockback: 0%
Move speed: -20%
Special: Heals up to 25% of player's HP, at the cost of 1% durability per HP.
Grappling Shoes (any common boots + TT, pseudo-gothic boots):
Armor: Original
Durability: Original
Knockback: Original-50% (if possible, max -90%)
Move speed: -10% (since common boots are always 0% normal)
Hyperblaster (plasma rifle + ATT, pseudo-laser rifle):
Damage: 2d4x3
Clip size: 45
Fire time: 0.50s
Reload time: 2.5s
Accuracy: +8
Alt. fire: chainfire
Slugshot (double shotgun + PPA, pseudo-super shotgun):
Damage: 9d5x3
Clip size: 2
Fire time: 1.0s
Reload time: 2.0s
Accuracy: N/A (double's spread, normal's drop-off)
Alt. fire/reload: single shot/load
Carbonite Armor (blue armor + PAT, pseudo-phaseshift armor):
Carbonite Gear [1/2]
Armor: 4
Durability: 150%
Knockback: 0%
Move speed: +15%
Carbonite Boots (plasteel + PAT, pseudo-phaseshift boots):
Carbonite Gear [2/2]
Armor: 4
Durability: 150%
Knockback: 0%
Move speed: +15%
Complete Carbonite Gear provides floating over environment, as with phaseshift set. (If this is impossible, maybe make environment damage halved while wearing each piece (like ITYTD), so quartered for the whole set.)
Tesla Zapper (plasma rifle + ABBF (or ABBB), pseudo-Railgun)
Damage: 3d2x10 (damage type: fire)
Clip size: 80
Fire time: 1.2s
Reload time: 3.0s
Accuracy: +4
Special: penetration (if possible, make it look like shambler missile but fast/rapid)
Mass Driver (chaingun + PBBS (or PABB), pseudo-Railgun)
Damage: 7d7
Clip size: 70
Shot cost: 7
Fire time: 1.5s
Reload time: 2.5s
Accuracy: +5 (or 100%)
Special: penetration (if possible, half damage after first target, etc)
Targeted Launcher (rocket launcher + AATS (or AAAT), pseudo-Rev Launcher)
Damage: 6d6
Clip size: 1
Fire time: 1.0s
Reload time: 1.5s
Accuracy: +6 (or 100%)
Explosion radius: 3
Special: homing
Successive Shotgun (normal/combat shotgun + PBBF (or PBBB), pseudo-Pancor)
Damage: 8d3x3
Clip size: 9
Fire time: 1.0s
Reload time: 2.5s
Accuracy: N/A (original weapon's spread and drop-off)
Alt. fire: single shot
And for some just plain original ones:
Sniper Scope (sniping) (any bullet weapon + ATS)
All stats are same as original (other than big accuracy boost if not 100%)
Sight radius while holding weapon is increased by one (or two, dunno if one is too weak).
Acidic Formula (acidic) (any plasma weapon + PPF)
All stats are same as original (maybe a power/shot boost based on mods used)
Any tile in which damage is dealt creates a zero-tile explosion that covers it in acid.
Molotov Cocktail (combat knife + TT)
Damage: 1d2 (not meant for melee)
Attack speed: 1.0s
Accuracy: +4
Alt fire: Throw (tile in which damage is dealt (or where it lands, if possible) creates a two-tile explosion that covers it in lava)
If it's possible to make the throw damage/accuracy separate from the melee, I'd make the throw damage of the Molotov Cocktail higher than 1d2. In addition, I suggest making a Spiral Razor assembly that has maybe 4d5 throw damage and a really high throw accuracy.
Another possible upgrade to the assembly system is allowing more than one combination of mods. This would be very limited to considerations like swapping out S for A in ranged, accurate weapons for 100% accuracy (instead of whatever they had) or F for P/B for an extra x2 shots. Rather than requiring the rarer mods, they could be used to complement a particular assembly instead. (Alternatively, you could allow F/S mods to be the only possible additions to assembled gear, and remove F/S requirements altogether.)
Since this is the "assembly request" thread, I'd also like to suggest some balancing tweaks for what's currently in the game. (Spoiler'd just in case.)
In general, I'm wondering if you can fix the current assemblies so that the order of modding doesn't matter. I THINK that it's just a matter of what stats you're changing on the equipment when the assembly process occurs, so if you could lock all of them in (and pick some of the typical mod bonuses with it) it'd make carrying around the mods less necessary.
Gatling Gun could use a LITTLE boost in damage (to 1d7). Making it equivalent to the plasma rifle (sans damage type) will make it more appealing, especially on easier difficulties.
Tactical Rocket Launcher should still be 6d6 damage (like the original RL), since its primary function is wall-busting anyway. The large decrease in explosion radius doesn't mean it has to hurt any less, and I've found I almost ALWAYS have to use it twice to blow open a hole, whereas a typical RL is almost certain to destroy some wall in a single shot.
Energy Pistol is a little disappointing given the sniper mod needed: I was expecting regeneration, but simply increasing the clip size to blaster's (20) would be worthy of the mods necessary. EDIT: Nevermind, in practice the plasma damage makes a huge difference.
VBFG9000 takes FOREVER to reload its ammo. Maybe you could boost the ammo regeneration to 2 per action (or drop the capacity to 50)?