@mingbo and I have talked about this a few times. I don’t think increasing the timeout will solve the problem, as there will always be larger studies with more files.
I think we should either change the process to upload the files one by one and update the runs to use those files similar to how we do it in the sample workflows like this (How to submit an energy simulation to Pollination using the API - #9 by mostapha) or provide a solution to upload the files separately to your project first, and then use the reference to those files to set up the runs quickly.