Fitter is off by one or two ALUTs?

This is most likely an issue with LAB-wide control signals. There are only so many per lab, and although the issue is usually due to clock enables, I'm guessing you're hand-controlling synthesis, and it could be due to about anything.

Anyway, for starters, look at the fitter report -> Resource Section -> Control Signals and see how many control signals are being used, just for a rough idea.

Does this design fit without any location constraints?

My concern is that, since you're seemingly able to pack full 48,350 ALUTs without problem, I'm guessing there is nothing special about those final two ALUTs that you're trying to pack. Don't know for sure though. One test to make sure is to remove some(or all) of the logic except for these two LABs that have the dedicated logic, and then pack them full. If they fit, then there shouldn't be anything illegal that you're trying to do.

Another thought is that the fitter may be packing before it gets to your location assignmnets, i.e. it packs everything as it thinks fit, and would then re-arrange those packings based on your assignmnets. If that were the case, this initial algorithm may have it's own no-fit(due to LAB control signals) and give this error, even if you theoretically had a viable packing/placement scheme that would work.

Finally, you'll probably find that this running out of labs message isn't the most detailed. The reason is that the user normally doesn't control the LAB packing or really understand it. So if the fitter over-runs the number of LABs required due to packing, it would need a detailed report on all 3023+ labs and what's in them and what control signals they use in order for a user to try and find a "better" packing that might reduce the LAB usage. On most designs(probably all designs except this one), the user wouldn't have any clue how to find a better packing, and their time would be much better spent taking out a few ALUTs of logic or trying to find a better synthesis.