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I just put on an Edelbrock 1406 on my 360 and had to do some jerry riggin on the kick down linkage but I don't think this is my problem. The shift points have changed on my C6 and the thing has to be screaming the RPM to get it to shift into (D). It works better if I manually shift each gear myself. I have it scheduled for a flush in the AM but would like some input before that. The truck has 107 original miles with dad only driving it short runs for years but I now use it alot and there is a small drip under the truck. Everyone says these guys can take alot and the shop says I can get a rebuilt for around $700 but it makes me nervous. An other shop sats I must change the filter after 100,000 period. Let me know! This is unchartered ground.
A c6 can handle quite a lot. (except reverse) anyway, a flush is not a bad idea, but I am wondering about the correlation between the carb installation and the tranny. It sounds as though there is a vacuum problem. Check and/or replace all the vacuum hoses and their connection points.
A rebuild may be an option, if so put in a shift kit to improve the shifts and prolong the life of the tranny.
Lastly, I have driven many a ford auto shifting them manually. Never seemed to hurt them, still doing it today (out of necessity).
The change in manifold has changed the manifold vacume - which is used by the tranny to set the shift points. You can adjust this with a small screwdriver inserted into the port where the vacume line connects to the tranny (on most of them). Do a search as this has been covered many times and there are many experts on this board.
As to the filter, I changed mine out at 50K, and at the same time added a drain plug to the pan - and never changed it again. I now have 260K on the transmission. Unless you have expensive problems you will never see any dirt or metal shavings in the filter.
If everything was good before the carb swap, you need to look at the vacuum lines that connect to the transmission's vacuum modulator valve. More than likely, you have manipulated the line enough during the change to crack hose or pull it loose from it's nipple. The line should be connected to the valve on the right rear of the tranny above the pan and may or may not have a metal line it connects to that makes it's way along the transmission to the engine compartment at the back of the engine. If you have the metal line, you will have two hoses connected to it, one at the modulator valve end and one at the engine compartment end. If no metal line, it will be a long single hose. Vacuum test the hose from the engine end to evaluate whether it will hold a vacuum. If not test the modulator valve itself to see if it will hold a vacuum. If not, replace the valve. If the valve holds, replace the hose.
Mine sort of did the same thing when I replaced my carb, sounds kinda silly now but you said you had to do some rigging to get it to work, you didn't by any chance tie your old downshift linkage off the carb, up and out of the way did you? Did it to mine, it wouldn't hardly shift unless it was tachin about 2500, it would shift manually though, I had the linkage hung right in the middle where it wouldn't shift on its own but you could make it, that's what kept throwing me off, mine had been sitting awhile and I just though it was gummed up alittle. So you might check that, and remove it completely from the tranny even if its not binding now, it could at the worst possible time!!!
I initially used zip ties to hold the kick down linkage to the throttle linkage only so it would not rattle since I removed the old linkage bracket because there was no longer a use for it. I was afraid the kick down needed more independent movement bit if you look at the original bracket they move together anyway. I think what the problem is is that after talking to a mechanic friend is a selenoid or sending unit on the transmission. He says the way the shift points have changed that could be it.
There is a metal line coming off what appears the top of the bell housing behind the intake manifold without any hose attached to it. Nothing that I took off has been attached to it so I thought maybe it is a vent of some sort. Is this a possible culprit? A mechanic friend thought there is a selenoid or sending unit at the transmission. The other thing I noticed today while in traffic was it felt like it was creeping in a non fluid manner which made me think the bands were going out.!!!!!!!
Trace that metal line and see if it goes to the modulator valve on the right rear of tranny. There should be a rubber hose on that end that is turned like a "U" on that end where it connects to the valve. If that is where it traces to attach a length of vacuum hose to the other end at the top of the bell housing and the other end to a intake manifold port and you should be shifting better.
If it is a small steel line it is the vacuum supply line for the valve. If it is a large metal tube (about dime size) it's the transmission dip stick tube so don't suck the tranny fluid into the intake! Put that dip stick back! LOL