Our $.02 worth: As others have suggested, your lights are probably not the issue. SPS are very sensitive to movement/handling and some take a long time to adjust. Proper acclimination is the key here.
Assuming water parameters are in line (which appears to be the case here), issues such as water flow/placement also come into play. And, as mentioned above, all of the other inhabitants in the 'new' environment also come into play.
That being said, I would also suspect the presence of the 'un-happy' Leather as part of your problem(s). As far as the sponge is concerned, you're probably OK doing that. The down-side is that as it gets 'dirty', it becomes a little 'nitrate-factory'. Though, if kept clean, this isn't the case.
Also, 5 weeks is a little 'young' for a tank with SPS. Rule-of-Thumb we heard is 12 months. Likely, the new LR, the fresh tank, the un-happy Leather, the movement/handling of the SPS, and the medication(s) are all contributers to stress for the SPS.
In any case, if the SPS tissue looks healthy and all water params stay as good as they are now, you should be OK. Keep up with your Skimming, add Charcoal 24/7, and consider routine water changes, as appropriate.