It is odd to me that the clip caused the binding, if anything I would think that the clip would act as a spacer and give you more room on your bolt-to-screw clearance. If it were me I would either shoot as is without clip and see how it shoots, or file a bit off of the pillar to get it flush with the wood and then put the clip back in as it's supposed to be.
Worst case scenario you end up having to glass bed it. There are plenty of threads floating around here describing how to glass bed it yourself so you don't have to pay a pro to do it for you.
On mine, my pillars were just a fuzz short of being flush. After snugging the action a couple of times they mated up very nicely so I went ahead and epoxied in the pillars. You may also want to file just a bit off the threaded ends of your 2 action screws, if they are that close to causing your bolt to drag a lil' extra room won't hurt.
Also watch the trigger well area, both of the Hart LRT's that I have used were very close to the trigger and cause stiff triggers or even on one of them it locked the trigger. Used the dremel and cleaned up the trigger well and all was good. Wasn't much, but just enough to cause issues.
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