Pull the low liner and clean the seat. Recheck height then fit a shim of suitable size. Volvo diesel trucks use this method. They use oring seal on the lower end of the liner and a very small o ring or silicone sealant under the top edge of the liner.Shim is steel not copper. Adjust to suit the correct liner height. May need to do all three.
Are you sure you've not disturbed the liners when removing the head? My Daytona uses the same setup (liners just siliconed in the the block at the base) and it's quite easy to pull the liners about when you remove the head. Triumph have a "special over priced tool" to stop it happening.
If it were my bike I'd be pulling out the liners, measuring they're all the same height, cleaning up the liner sealing area in the block and try to find any discrepancies there. You can then place all the liners back in the block without any sealant and check the heights again.
lazyb I feel that you are right it requires a methodical approach, first find the cause then sort out the cure.
Measuring from block seat to deck height on all 3 any error ? measure liners lower seal face to top face any error ?
If machining error on block CKJDs solution sounds OK & cheapest , the expensive way have a Good machine shop correct the seating faces then skim block face correct level Presumably .005th
Best of luck
Hmmm good answers,thanks lads...i have,nt disturbed the liners and there still stuck fast, what i was trying to avoid is splitting the cases but looks like its going to happen...Also a big thanks for the service book links but i have the same factory service manual in paper form