Vanagon GL, 2.1, 1986

This has been taking place for a while now ... those who remember my
problems after the alternator burned.
Anyway,

Problem 1:  I don't seem to be able to smooth down the idle. It is kind
of erratic and the engine kinda bounces around a bit. Even the people
driving behind me have told me so. If you raise the idle, it runs
smooth. Suggestions?

Problem 2:  When changing gears from 2nd to 3rd and 3rd to 4th
performance drops. Actually, changing from 2nd to 3rd, it feels like
changing from 2nd directly to 4th. It works great and is very powerful
in 1st and 2nd. In order for gears 3rd & 4th to change without losing
much pick up, the RPMs have to be maxed out (more than 4,500rpm, beyond
the green safety area). After it picks up speed, it runs smoothly but as
strong.
Suggestions?

Now, here are the parts that I replaced with brand new dealer parts:
ECU (because it got fried when alternator fried)
AFM
Idle Stabilizer Control Valve
Idle Stabilizer Control Unit
Oxygen Sensor
Temperature Sender II
Distributor cap
Distributor rotor
Ignition Wires
Spark plugs
Temperature Sender for Gauge
Relays
Alternator
Red Wire (because it fried when alternator fried) from alternator to
Vacuum Hose Routing Diagram box, where the blue wire from the alternator
ends up as well.

I checked for air leaks or any other types of leaks. Nothing that I
could locate.
I checked the grounds that I could locate.
Ignition timing is good.
Idle RPM at 880
Fuel injectors are good.
Throttle valve switch is good.

Never had any problems before. Everything started when alternator fried.