G'Day Doc,
Having ridden the other "standard" RL up here, I don't think the cover makes too much of a difference, though I can see the problems the standand pushrod system might get as you described. If I was you, I'd take out 3 springs from your clutch and give that a go. The TM cover is also big, and a bit precarious when riding in a rocky section.
Cheers,
Ben