I Highly Recommend Several Upgrades To The Transmission. First, Get Rid Of The Stock Cooler.
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..........IT IS WORTH IT.
An auxiliary cooler is a good idea if you drive under load as a regular trip. Beyond that, the factory cooler will work fine. If you want to add a cooler, it can't hurt.
If the little balls in the trans "melt", the trans was well beyond too hot, and you should change your fluid immediately.
If your cooler clogs with clutch material, you have bigger problems than what will happen when the cooler plugs up.
Shimming the trans away from the engine may be necessary, but check with the supplier of the flexplate. If you need to shim 1/16th of an inch, use .062" shims.
Nine discs in the front clutches is nearly impossible. Six, maybe seven might happen. But in order to do so, thickness of the drive and friction plates is compromised. A stock 48RE has 5 and 4, front and rear. The OD housing has 6 discs for OD, and 23 (count half that for an accurate comparison with the other clutch packs) single sided discs in direct.
The 48RE does have 6 pinion plantetaries. I've also heard that some builders prefer the 5 pinion plantetaries.
A VB upgrade is a good idea. There are several areas which can be improved. Details can be found in various shift kits. The advice to go with something less than a full race shift is a good idea.
Ultimately, find a good trans builder, and follow their advice. Stay with their product through the entire trans, TC and VB. Don't mix and match.