My MNK tanking tips:
In general, yes, MNK tanking in Abyssea is more about Counterstance and being curebombed. If your WHM is paying attention, you're good. Do damage, keep hate, try to reduce mob TP. That's the basics.
1) Look into appropriate elemental resist atma (e.g. Brother Wolf for fire, Ascending one for wind, etc.), which are hugely useful on specific mobs that have those elemental attacks. Otherwise, Gnarled Horn is huge for AGI/Counter/Crit rate. I usually default to RR/GH/Apoc, but I'll ditch Apoc or even RR sometimes for elemental resist. I always use GH when tanking though. You might even use a max HP+ atma if you have mages who are on the ball with curebombing you.
2) Don't discount Subtle Blow. You're likely one of the only people TPing on an NM if tanking something hard on MNK, so reduce the amount of TP moves you need to deal with. SB cap is 50, and you'll have SB+20 from traits. I personally TP in SB+20 from gear (Rajas/Tantra+2 Head/Black Belt), which along with Auspice from a WHM (base SB+10, and raised to SB+15/20 if the WHM has Orison +1/+2 feet) puts me at cap. Other nice gear options include Agasaya's Collar and Heed Ring (SB+7 and Eva/Acc+3, definitely a great option particularly if you don't have Epona).
Also, remember the relatively recent change that AGI now affects the amount of TP given to the enemy. Another great benefit to GH atma. Add in Penance/Chi Blast, NINs using Yurin, and BLUs using Reaving Wind, and you can really significantly reduce the amount of TP moves.
3) You also will likely want to look into a DT- macro set (particularly MDT-) for things you can see coming and just have to eat. Twilight Torque is particularly nice for this, as are augmented Dark Rings from gold boxes in [A] Konschtat. I don't personally go as crazy with a DT- set as some people, but it's nice to at least have a few good pieces to macro in for those osh*t moments.
4) Subjob: /WAR is ideal with good healing, but for (a) some particularly nasty mobs with attacks that are absorbed by shadows and (b) situations where your mages are slow, /NIN is good. Perfect Counter is great for reapplying shadows. I tend to default to /NIN unless I really trust the healer. /DNC can be nice for a lowman setup, more for Violent Flourish stun than anything else (but Haste Samba and Waltzes certainly are nice to have handy).
5) Merits: Your group 1 choices are the standard. For group 2, the more common setup is to go 5/5 Penance, but you can live with 4/5 if you really love soloing with Invigorate. I personally ditched Formless and never looked back, and just went 5/5 Penance AND Invigorate. I don't miss Formless a bit - it gimps your damage anyway and even if a mob becomes immune to physical damage it's silly to think your MNK melee is going to be a huge difference by putting a tiny dent with Formless damage (to do any significant damage you'll generally be relying on nukes anyway).
6) Weapon: Lacking Empy/WoE/relic, I vote Str/Atk. Keep hate off those BLMs trying for yellow procs ;) Taurine Cesti were pretty nice at 90cap, good damage and the Subtle Blow helped. But now at 95, the Fire path claws are pulling away a bit more.
7) Be sure you have as many of the 6 Abyssites of Merit as possible, for better Cruor HP buffs.
Anza: Titan 2004-2011 / Capuchin: Phoenix 2011-???