The problem with the 42RLE in 2005/2006 isn't with the transmission itself it's with the transmission control module (AKA TCM) that was separate from the PCM in 2003-2004 but moved inside of the PCM (engine computer) for the 2005-2006 models. That's when the TCM developed a heat issue that can cause it to blow like an M-80 firecracker went off inside the PCM. There is a fix for that from
www.wranglerfix.com that requires replacing it with a different model PCM but...
I currently drive a 2004 with the 42RLE and it works well but I still miss my previous (stolen) TJ with the 32RH 3-speed automatic which is pretty much as close to bulletproof as they come.
The other potential problem with the 2005/2006 models is the OPDA (oil pump drive assembly) that was redesigned for 2005. It has a lubrication problem that can cause cam and oil pump drive wear issues but I have read where that problem was mostly eliminated in later 2006 models.