I just reread your post.

Looks like your engine is scooted all the way back on the mount. Is that the correct distance the manual calls for? If it is move the engine forward on the mount a bit (away from the firewall) just enought to clear the fourth bolt I'm sure the extra few millimeters won't be that big a deal and won't have a negative effect. Also, why are you inverting the engine? How about a sideways install? Would that make for an easier throttle linkage installation? Yes, I'd use all four engine mount bolts.