HI and welcome to the site. Good to have you aboard.
As Phatdaddy has said, Photobucket is now charging for use of their site. Use Imgur instead. Works better and it's free.
As far as the height goes, it's inconsequential for performance, but the higher height of the 25" will keep more water out of your engine and boat. It's the main reason manufacturers switched to the 25" and even the 30" transoms.
As far as the transom goes I personally prefer the pourable type. If you want to replace the transom with a new wood core you'll have to cut out the inside fiberglass skin for access. (NEVER CUT THE OUTER SKIN) With the pourable you just need to remove the old wood between the inner and outer skins. (chainsaw and a long flat skinny piece of metal with a "L" bend on the end will become your best friends) Much easier and no problems with trying to get the proper curves in the new wood, etc. Plus, you'll never have to worry about the transom rotting ever again. Yes, pourable will probably cost a little more, but it's a small price for the peace of mind.
As far as the floor goes, that can be caused by rotted stringers or rotted wood under the deck. (or both) It will involve removing the deck to accurately determine the cause. The fix is straight forward in both cases. Just remove the rot and replace with new wood. (Use pressure treated or marine grade.
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1987 V20 w/1987 150HP Yamaha on a Shoreland'r Trailer
1978 16.5 Airslot w/1996 120HP Force on a Four Winns trailer
1996 V21 w/1993 200HP Mercury on a Shoreline Trailer
All towed by a 5.7L Hemi Durango.
If God didn't have a purpose for us we wouldn't be here, so
Live simply, Love generously, Care deeply, Speak kindly.
(Leave the rest to God) 
Silence, in the face of evil, is itself evil. Not to speak is to speak, not to act is to act. God will not hold us guiltless.
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