IMHO K&N pancakes won't stop you getting it tuned, whether or not they offer any performance benefit or not is another question - but do make sure they are clean and free-flowing.
I've been more than happy with the tune-ability of my 1500 engine on K&N filters over the years, all of this "not original, you won't get it tuned right" has a grain of truth, but anything that's not as per factory will cause just as much (if not more) trouble. eg. worn carbs, damaged/worn/tired carbs springs, leaking manifolds, leaking breather systems, etc etc.
I think the bigger issue is the use of HS4/SU carbs. and the question of whether HS4 are "big enough" for that engine - and then choosing the right needle.
I guess we need to start with "what's wrong with it right now?" The "sometimes good, sometimes bad" nature of the running issues suggest it's not something fundamentally wrong with your set-up but that you have an intermittent fault?
Provided HS4s flow enough for the engine a good rolling road familiar with SU carbs should be able to grind a set of custom needles to give spot on tuning, but that's really not an "on the drive" DIY job!