So I'm gonna start with topic B: Upgrading a necrocraft. I think I'm correct with the RAW, to updrage your necrocraft from HD 4 Medium to HD 7 Large, you'd need 9 extra corpses since the medium necrocraft only counts as one for the 5-100 undead you need to make the monstrosity. Then from HD 7 Large, to HD 10 Huge would take 23 extra corpses sinepce a large counts as 2 mediums. However with this "upgrading" method you could keep the same CP spent (you wouldn't need a new ghoul for ghoul parts for example), instead gaining the difference or letting you "retrain" his CP if you wanted to change things.
If I'm wrong, and upgrading requires less undead, I.E. the necrocraft counts as all the corpses used to make it (requiring less new material) let me know? However onto the main question.
Making a higher HD, higher CP, medium necrocraft. There's a brief excerpt in the monster's entry about giving them more CP than their size, and increasing their CR by 1 for each CP boost, however this seems to be only a GM tool. It then goes on to describe "Necrocrafts are better suited for brute force than delicate manipulation, and most creators build larger hulks rather than smaller, more agile (and fragile) necrocrafts." However as a neutral adventurer with a purpose for the necrocraft, mainly being party hit sponge, I won't be able to fit a huge or larger undead monster into the tight confines of a dungeon. However, a 4 HD undead will lack the BAB to hit anything in higher levels, accompishing his grabbing style to peel things off the wizard, alchemist and cleric (or gunslinger if something ever got close enough. We're a very melee-unfriendly party).
One way I've considered to bypass this would be Reduce Person with some Permanency. Make the large then shrink it, but to my knowledge you can't shrink the target more than one size category, and you can't reduce him twice, permanent or otherwise (can't overlap the same spell on someone). So I'm at a conundrum of not wanting to make something enormous that's no use to me, yet also wanting to maintain the party's bodyguard when we finally hit levels 7, 10, 14 and 18. Can you make a better, Medium necrocraft? Or is there some method I'm overlooking to after-the-fact shrink them?
There isn't really an 'upgrade' a necrocraft. You have what you make them as, although you can use an existing necrocraft as your first paragraph talks about.
Reduce person won't work on a necrocraft, since it only works on humaniods, not undead. You would probably be better off finding something suitably tough and making it a zombie or a skeleton (bloody skeleton is often a favorite.) Even a few 1 HD bloody skeletons in front you you can buy you an extra round. Also, a large creature can squeeze through a 5' corridor, not much good in a fight there, but often even in dungeons the fighting is in larger rooms.