I solo'd nearly the entire Windurst path on BLU (duo'd Howl from the Heavens with a WHM, stupid wards have the HP of a Taru BRD30...). Also had to solo the latter half of San d'Oria's path since my LS static for these missions fell apart shortly after completing WotG via Bastok's quest line. Seemed like I was the only one interested in doing these for the story. =/
The only other time Windurst's quests gave me trouble was in The Long March North. That took me three tries, but that was primarily because I screwed up the first two with misjudging Dream Flower range (Ahrimans were out of range and slept me before I could poison myself to avoid Sleepga) and in the second attempt the boss woke up before I finished with his minions. Other than that, I effortlessly blitzed through these quests, even the final two battles, which took like three minutes each. Surprised by how weak they turned out to be.
Each nation path seems to have that one mission that stands out as much harder than the rest, and they're all at the same point (Quest 11, as shown on the wiki's mission page
). I'd say that San d'Oria's Blood of Heroes is the hardest of the three. I needed to drag some LS mates up to that point just to finish it. Then I just breezed through the remaining missions solo. San d'Orias Bonds That Never Die might give you some trouble, but you can probably zerg that down on SAM.
I'm not so sure about Bastok's path since I finished that long ago at 75 with a static, but looking through the missions again, they don't seem like they'd be too difficult for a 99 with your jobs. Maybe some difficulty with What Price Loyalty and Bonds of Mythril?
As for the main missions themselves, I don't think you should have that much trouble until perhaps Darkness Descends. Though a friend just solo'd that on SCH by just keeping the NPC cured. Only other potentially difficult one is When Wills Collide. You face four enemies at once. You can solo this by having a supply of Reraise and fighting by the entrance. Kill one or two, die, reraise and repeat. The final battle should be simple on BST.
Overall, if you're just looking to finish through one path, I'd highly recommend Windurst's. The two quests which might give you trouble aren't in battlefields, so anyone can help.