Hi Kevin,
a few things to try:
1. Re-generate the genome index without --genomeChrBinNbits 0 . The default value of this parameter should work fine.
2. If this does not help, please try to map a "good" human or mouse dataset (e.g. ENCODE) to your combined genome and check the speed. This will check whether this slowdown is specific to your sample.
3. If good dataset maps fast, then the slowdown is likely caused by reads that map poorly in your dataset. In this case, please try reducing --seedPerWindowNmax from the deafult of 50 to 30 or even lower 20,10.
Cheers
Alex