Toyota compensated for the 4 spd auto by using one gear set taller than the manual for the same size tire. For instance with the 28" tire/5spd manual you had 4.10's, for the auto you had 4.30's, and for 31" tires you had 4.56 gears for the 5-spd and 4.87's for the auto. The 4spd auto has always had less power and worse gas mileage than the 5-spd do to the rather tall gearing.

While you are creating longer gears, you don't have the HP to support those longer gears, which will make taking off from a stop/or slow down seem like you are towing a heavy trailer. This is why you loose 5th gear on the highway, and is why you will be going through clutches quicker than usual. If you had an engine w/about 400hp or a truck that weighed less than 1500lbs, you wouldn't have much of an issue, but you don't.

Pulling a spark plug will give you a pretty good idea of what it is going to be like w/4.10's and 35's. I have 5.29's/heavy sticky 35's on my '91 5-spd w/ new motor(less than 5k) and it is a slow, I couldn't imagine how much slower it would be w/4.10's.