As long as you keep the cat in place there should be no issues.
The midpipe on the 35i has far less silencing than the midpipe on the 40i, deleting the small resonator, either cut and weld or with a fabricated new section isn't going to make that much difference.
The mpe on the 35i is better than the 40i as it retains the valve, that's the way I'd go.
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