I like this mod, optimisation is very much a needed thing for Minecraft, however, while using this mod I noticed the mending enchantment was repairing my tools incredibly slowly. I then disabled the mod and it was fine.
This issue looks like it's being casued by the enchantment only repairing your tools for every xp orb you collect, and since they're all clumped into one orb, you only get one set amount of repair.
You should be able to fix this by changing the mending enchant to work based on how much xp is in the orb, rather than the amount of orbs being collected.
While mending is moslty for vanilla use, in lighter modpacks and even with popular mods like Tinker's Construct I can see this being an issue. Please fix this as I'd like to continue using this mod.

MC version?
Clumps version?

Here is a side by side comparison of Clumps (on the left) and Vanilla (on the right).

https://www.youtube.com/watch?v=_0Bo2yb63Eo

Here are the stats from that video.

Start:
  Clumps:
    offhand: 561
    mainhand: 561
    helmet: 63
    chestplate: 228
    leggings: 195
    boots: 129

  Vanilla:
    offhand: 561
    mainhand: 561
    helmet: 63
    chestplate: 228
    leggings: 195
    boots: 129

End:
  Clumps:
    offhand: 679
    mainhand: 713
    helmet: 227
    chestplate: 318
    leggings: 381
    boots: 331

  Vanilla:
    offhand: 653
    mainhand: 649
    helmet: 215
    chestplate: 358
    leggings: 399
    boots: 305

Differences:
  Clumps:
    offhand: 118
    mainhand: 152
    helmet: 164
    chestplate: 90
    leggings: 186
    boots: 202
    total_mending_done: 912

  Vanilla:
    offhand: 92
    mainhand: 88
    helmet: 164
    chestplate: 130
    leggings: 204
    boots: 176
    total_mending_done: 854

The way that vanilla converts experience to damage is by just doubling it, so 1 experience will mend 2 damage.

So if we take our totals of 912 and 854 for Clumps and Vanilla respectively, we can see that the Clumps orbs had a value of 456 and the Vanilla orbs had a combined value of 427.

From here we can calculate the average experienced spawned for each test.
The average for the Clumps test is 7.125 (456/64).
The average for the Vanilla test is 6.671875 (427/64).

As stated on the Minecraft wiki here, the bottle o' enchanting on average spawns orbs with an average value of 7.
Which is more or less what both test showed (although the Clumps test was a bit higher, I'm sure if one had to do more tests they would see that it is the same).

I don't know what to tell you, but the logic emulates vanilla's mending nearly perfectly (if not perfect).

since it's prioritising main hand over off hand.

There is no prioritisation at all, it gets any item with the mending enchantment in the player's equipment slots (armor, mainhand and offhand) and repairs it.

Could you upload your latest.log file to pastebin so I can take a look at it?
Just want to see if there are maybe any other mods installed that may be causing issues

So your first log doesn't mention Clumps at all, can you go in a world, and hold "f3 +c", it should crash the game after a few seconds, can you upload the log from that crash please

So I don't see anything that would cause issues.

I honestly don't have an answer for you unfortunately.

Does your armor maybe have mending which would be using some of the experience?

Only other thing I could think of would be something to do with LAN, which isn't supported (as in, if it works, great, if not, there is nothing I can do to make it work).

Can you reproduce without LAN?

If it has mending, it does take away a chance for other items to be repaired, so it is possible that is what was happening?

But yea, I can't reproduce this, so I can't really fix it. Sorry.