Apply a little heat to the plugs with a propane torch and they'll come right out.  They should be installed with something like Permatex Aviation Form-A-Gasket.  I've never used Locktite on those and never had one back out.  I'm not super confident in Locktite's ability to be oil tight (it probably is, but I know for 100% certain that Form-A-Gasket is). 

The bores are probably not tapped deep enough to allow them to sit flush.  When I tap those passages in an engine that had press in plugs I run the tap in a bit, test fit the plug, and continue tapping if needed to get them flush.  The only caveat to that is beware of intersecting oil passages.  You don't want to allow the plug to seat too deeply and risk blocking an oil passage.  Sort of academic, at this point I certainly don't recommend trying to tap the holes any deeper due to the risk of metal shavings getting into the engine.  I'd just remove the plugs and grind them down as needed. 

How much of an interference are we talking about?.050", an eighth inch? Lay a straight edge across to check the interference. If it's just a bit, can't you clearance them while they're still in the block? Just don't knock them down to where an allen wrench can't get a good grip.

If you put a straight edge across the  block they stick out maybe just over 1/16".  where they interfere is the block plate that goes on before the flywheel.

 

My Keith Craft DART block had same issue.  I took a cutoff wheel to the block plate and removed that area.  No problem!

If you have a DART block, did you check for timing chain clearance?  Note I had to grind the aluminum block for the chain to not rub it.  All parts were supplied by Keith Craft.  I have also experienced this with original 351W blocks.  That is why I know to CHECK EVERYTHING before assembling an engine.