Re: Gratting noise
The 5-45RFE tranny uses 2 filters, a round spin-on cooler return filter and an oval inlet filter. Both are inside the trannypan. Take care when installing the new oval filter, the seal should be placed in the pump inlet first and completely seated with the help of the buttend of a hammer for example, and then the filter can be installed. Not obeying this, could result in a disconnected filter and no fluid to the pump, with eventual further tranny damage. Also take care to have the right tool to remove the spin-on filter, it can be quite fixed in place.
Regarding your other questions, i can´t help you. You could maybe also ask this in the WJ section.