Main Saddles

I have a KB Stage 3 block that had some main journal repair. Unfortunately they cut the block leaving the caps at full height. This has created two issues, The journals are .028" deeper into the block, the gear drive is correctable (barely) with an undersized gear but I have been running a 4.5" crank and in my precious Block could get the Rods past the cam but not in this block. So one option is to fix the block, can all journals have saddles and still be considered a sound engine? Additionally the rear seal will need to be welded and re machined I presume.
Combo is a Blown Alc /converter, Quick series type setup (2000hp ish)

 

Seen blocks with them. But it depends on how times a block has been welded up ect. Especially if it’s a water block?