rds - Yep, good points WRT transistor height... I too always left room under for airflow but whether that is truly a heat-diss. advantage is unclear.
As far as getting them that low, the PCB is designed for the "triangle" base pin TO92 layout not the in-line one (tech terms escape me:) I don't pre-bend, although that may be good to do, I find the leads have enough flex to get them pretty close to the board if you want.
grounds - like rds says but I'd always ground the pot if its not going into grounded metal.
Lil Knight - Yep, as before the board is tight for sure & this PCB rev is better than the last in that regard. One of the prime CTH goals was a full-featured, through-hole DIY desktop headamp in its 3" x 4.8" space (see 1st "A Very.." thread post). When you review its features, operating points, SQ as reported by owners, etc. it seems to have met & exceeded its design goals.
WRT C4 coupling caps I've heard most of the usual suspects in CTHs. This is really IMO but I'd not obsess about this. Reports say the amp sounds great w/any C4s used to date, but there are subtle diffs amongst them and you can find others' opinions in the "A Very.." & Tube and Tweak threads. My own experiences & opinion echos those like Lil Knight's above. Note: There is no reported lack of "crispness" for CTH, so IMO "slower" caps that trim upper-treble a wee bit are something to consider. But again IMO we're splitting hairs a bit here esp when you consider the many tube-rolling possibilities to get similar effect.
BTW fitting fancy caps is easier using the new PCB rev but keep in mind well-soldered & secured C4s are a must. Here's my latest, next-to-last CTH buildup (prior board rev):
Edited by cfcubed - 3/31/11 at 7:27am