The short ones are for lowering the roof for trailering/towing. If you change the short to raise it, if you tow it you will put excessive force on the bimini which its not designed to handle.
Does your fundeck have the round tubular poles or the square poles
For the round poles, you could check overtons or iboats online and see if they sell the bimini poles and simply cut the longer ones to length, and reattach the end caps, etc
The square ones, I'm not sure where you'd find them. You may need to find a metal fabrication shop to find those as I'm not sure anyone still uses/carries them.