Help!!!

Being new to this forum leaves me at a disadvantage. My problem may be listed somewhere on these pages that I just don't have time to seach through. A search of what I need doesn't turn up anything.

My 94 has just over 200,000 on the original 350. I replaced the intake with an Edelbrock and rebuilt the TBI unit some years back, along with an MSD coil, rotor and cap. I also installed a B&M shift kit with a deep sump trans pan. When cold the truck doesn't accelerate smoothly. It stumbles bad enough that I have to goose the throttle to keep it running. The truck flat spots for a few seconds before running "normally". Once warm it doesn't seem to happen again. Also, it has a hard time towing a 3500 pound load.

I have a 3:73 gear set. The rear end was rebuilt by 4 Wheel Parts 3 years ago. It has an Auburn limited slip with new ring and pinion. The whole set up has been howling since it was installed, mostly under load. They replaced the setup twice, with the same result. What would cause this? All bearings were replaced at the same time.

Welcome to AF.
If the rear end and is howling and not a tire howl it is not set up tight.
The ring gear and pion has to have Acceptable Contact Pattern to start with.
This link has some good info on it.
http://www.differentials.com/install.html

What MT says about the rear end is true. If it isn't set up right it's going to make noise!!.

You told us what you've done to the motor "some years ago" but you didn't say when the problems you described started happening?? 1st thing I'd check would be the CTS (Coolant Temp Sensor).