Checking the transmission fluid level is the first step, always. I presume that you've done that, in addition to establishing that it doesn't look dirty or smell bad.
700R4, 4L60, or 4L60E? Similar transmissions but the 4L60E has more electronic controls.
"Kinda chugs" is a vague description. What gear is the transmission in and how fast are you going? If it has a tach, does it do anything when "chugging"? Is there any dependence upon accelerator position or road speed?
The following is therefore a GUESS. I'm going to GUESS that your vehicle is old enough that it has the 700R4 or 4L60 (not E) transmission. If you had to change an intake manifold gasket, you would have had to take the intake manifold off, and therefore you would have had to take the throttle body off, and therefore you would have had to mess with the throttle cable ... and if the vehicle dates back to before the early/mid 1990s, you may have also had to touch the TV cable and might not have adjusted it properly. (The TV cable leads from the throttle body to the transmission, and that's how the controls inside the transmission know how much load the engine is under, and thus how much line pressure to use and alter which gear to select.)
If it has a TV cable, make sure it is (a) connected, (b) working, and (c) adjusted properly.
If it is mid-nineties or newer, it should have the 4L60E transmission, no TV cable, and it's all drive-by-wire. (doesn't mean there can't be anything wrong with it, but it changes the diagnostic method ... and it also means that the trans controls should be generating fault codes accessible by OBDII if there is something amiss)