904 transmission shift issues...

For sure you have a customized kick-down linkage since the slant didn't come with your Holley 4 barrel. If your 904 trans is OK, the problem is that your linkage is commanding kick-down even at low throttle. Is the kickdown pulled as far forward as possible (at the transmission), with a gap in the slot before the throttle starts to push it?

What size carb? If bigger than 370 cfm, you may have stumbling at first since it is likely too big for your engine. I doubt the stumbling has anything to do with the transmission.