2000 Olds Silhouette Shifts hard...sometimes....

Hi,
My 2000 Silhouette 3.4L V6 has about 151,000 miles. It is running great. But lately has developed an intermittent hard shifting while accelerating through all gears. I say intermittent because you can start the engine cold and it will shift smoothly the entire trip, be it a 10 minute drive or a two-hour drive. However, once you shut off the engine...maybe like for shopping or whatever....when you restart the already warm engine, the shifting will all be noticeably hard while accelerating through all gears. You will arrive at your destination, but you will feel every gear change when accelerating. Possibly there is a whining sound too, but not very obvious.
I've been reading some of the previous threads about the PCS as the likely culprit.... Would any of you have an opinion on that?
My check engine light has been on for a while, but the codes are related to emissions...secondary air pump, which I currently have disconnected because the pump is bad and I haven't had the desire to replace it, especially since it doesn't affect performance or driveability, as far as I can tell.
I don't believe my scan tool has the ability to read codes related to the transmission. Does that require a special code reader?
I read that the PCS replacement is a bit of a pain. I've done a good deal of repair jobs on various vehicles over the years, so I'm not afraid of a challenge. Nonetheless, I don't want to go to that effort without being pretty darn certain that the PCS is the real culprit here.
I appreciate any advice. Thanks.

All transmission codes are "P" codes, so your scan tool should be able to read them........

Certain transmission codes will not turn on the CE light right away, they are "pending" codes(have to fail twice in a row in a "drive cycle" to turn the light on).....

And sometimes, other codes will force the PCM to react differently, for example some codes will force the coolant fan to run....

Usually, when you are "feeling" hard shifts, that is because the PCM is commanding "full line pressure", which is usually a result of a code failure, even if the CE light is not on, there could be one in history....

Have you checked transmission fluid level and condition?

Thanks for the reply, Tech II.
Current codes are:
P0171 - System Too Lean Bank 1 (I have had this code off and on for years)
P0410 - Secondary Air Injection System
P0418 - Secondary Air Injection System Control A Circuit (I pulled the fuse on the secondary air pump)
P0452 - Evaporative Emissions System Pressure Sensor/Switch Low
Do any of these sound like they could relate to transmission issues? Again, thank you.

I wouldn't think, that any of those codes would affect the tranny...

Unfortunately, you would need a good scan tool, like a Tech II, to read transmission data, while the tranny is acting up.....you would need the scan tool attached, and go on a road test, and watch if full line pressure is being applied during shifts...

As for the last three codes, if your air pump works(comes on, on iniitial start up when the coolant temp is low), then the usual problem is the solenoid(has the sensor built into it).....

As for P0171, that is not a good code to ignore.....because, if the O2 sensor reads lean, it causes the PCM to run the engine richer, which is bad for your fuel economy, and can potentially take out your cat......

Regarding the P0171 - lean mixture bank 1, I've always suspected the culprit might be inadequate fuel pressure. Even after I had the fuel pump replaced, as well as the fuel pressure regulator, the fuel pressure at the fuel rail reads about 48, whereas I read that the needed fuel pressure should be between 52 and 59. So I really don't know what to do about that one....

Regarding the transmission, I may have to have a shop put a scanner on it.
Thanks again for the help.