I looked at your file.
Since your last tool is a taper I see that you are staying away from the walls .053" to not cut into where the tapered walls will be. That makes most of the middle pockets too small to get into for the 1/4" endmill - since they are only .351" wide. There are only 2 pockets that it can fit.
To get the 1/4" endmill to go into those 2 pockets switch your ramp style to “helix” and set the “minimum ramp diameter” to .05".
The type of ramp will stop the cutter from getting in some pockets if there is not enough room to make the ramp move.
Also it seems that the rest machining on the next tool does not know how much “stock to leave” was on the first tool - so you have to add that to the “rest machining” tool diameter in the second tool.
In order for the second cutter to know that you have left stock to leave on the first cutter - you need to add the cutter diameter to the stock to leave x 2. So the first cutter stock to leave was .053 so x 2 = .106" . Add that to .250" = .356"
That is the minimum diameter to put in the “rest machining” diameter on the second tool. I would add .010 for a safety margin. So .366" in the “rest machining” diameter on the second tool.
I ran it that way on your file and it all cleans up.
For you to see what is possible to machine with a 1/4" end mill just start by turning “stock to leave” off and putting ramp to “plunge”. Once you see what is possible then start adding stock to leave back on ( I know you need it in this case ). See what pockets are excluded by that. Then turn ramp on and play with the various types of ramp and size to see what that excludes.
Hey Chris, this does help! I really appreciate you explaining that. I didn’t realize I needed to add the STL to the tool diameter. Thanks again for your help!