Jeffrey: Different sail types may have different requirements.
Height of boom above deck
If your split junk rig is a McGalliard type, then it might have running parrel-downhauls. (Slieve’s notes Chapter 11)
If this is the case, then you need to allow for the parrel spans. The rule of thumb for this is: minimum distance between boom and deck = ½ x height of a sail panel, plus allowance for blocks. That's the minimum.
Otherwise I suppose its mainly a matter of visibility, headroom and sheeting considerations.
Height of masthead above the yard
If it is a low yard-angle sail (for example, the Amiina Mkll SJR) then it is tempting to make the mast not quite high enough, resulting in a halyard angle which becomes too great as you get near to raising the last bit of sail. You might have enough height to allow for the halyard span (for the 5-part halyard and its blocks), and enough drift to allow for the wringing effect as the yard moves from side to side – and yet, still not high enough, resulting in too great an angle between the halyard and the mast.
So, if in doubt, make the mast a little longer rather than a little shorter. Others can speak for other rigs, but I found with the Amiina Mkll SJR type, that for the sail to be easy to raise and for it to set nicely without the need for extra sail-setting parrels, the halyard block at the masthead must be at the very least as high as the peak of the yard, above deck. That’s an absolute minimum for that type of sail. That means a mast height a little more than might seem necessary at first glance. For a low yard-angle sail, don’t skimp on mast height.
(If your sail is some other type, such as the Johanna type with its somewhat higher yard angle, or a fanned type, with shorter yard, then maybe other criteria apply).
PS regarding your mast extension, you haven't said if it is at the foot or at the head. In any case, I think the experts would advise against welding. I have made a lapping masthead extension (aluminium tube inside aluminium tube) with epoxy (including a fairing between the two diameters) and it seems OK, but I am not totally happy with the idea, now. I was advised afterwards (and I think correctly) that a better glue for the purpose would be a polyurethane rubber type, such as Simsons. If it is a lap joint of 2' for a 5' pole then it will be plenty, plenty strong enough in bending. The other two forces are the "telescope effect" (axial, downwards) of the halyard - not so great in the general scheme of things - and the rotational forces of the yard - which ought not to be over-looked, but again well within the strength of a good polurethane rubber glue joint. Welding or mechanical fastenings are to be avoided except at the very top or the very bottom of the mast, in my opinion.