Whew! Talk about a bitsa!
You have no spigots on the top of the barrel then? A "spigot" is a rim around the top of the bore, cast into the iron of the barrel. They were phased out on later models. The matching heads had mating sockets to accept the spigots. There are aluminum rings available to fit into the sockets to return to the desired cr, if the head is spigotted and the barrel not. They have received mixed reviews.
I think
@Mike40M is very correct about checking your valve/piston clearances. I don't see how a 99 longer stroke crank in an 88 barrel would work without nonstandard pistons, and/or a
very thick head gasket. However, if there's damage to be done, since it's been run, the damage is done. This scenario would have been hard to foresee.
Pic of Model 7 and Mercury barrels and heads next to each other. While neither is an 88 or 99, they have the same barrel height and quantity of fins.
8 fins on the left and 9 on the right.
All this said, it doesn't quite add up that a long stroke crank in a short stroke barrel equals low compression, with all original working components otherwise, incorrect head gasket included.