Cheapskate Plenum Gasket fix?

The bolt length was originally intended to prevent overtightening, which damaged the factory gasket.
Hopefully you used a little blue LockTite on those bolts, since you shortened them, and they no longer bottom out securely.
Yours will probably be fine.
The best repair, meaning the longest lasting, is still to replace the stamped metal plate with a thick aluminum one. Versions are available from ebay for about 55 dollars.