Yup.. leave the perks. Makes a thankless job worthwhile and in the end will result in more B29s up for folks making those strat runs.
A few ideas on the HQ issue:
Double or triple the hardness or
add a dar ring around the place or
add a VH with a decent spawn or
add some soft guns or
change it from a single building to include the surrounding buildings
or max out the amount of auto ack (not puffy ack, the 37 and the 40s) to make a NOE run near impossible.
Those NOE lancs are a pain. The current way (at least on ndisles), a single player can keep the HQ down at the northern country no problem. Especially combined with the new .dt command.
The .dt command does take away from the fog of war but if we are going to make the towns resupply-able then it's needed.
Overall from what I saw this morning

to HTC! Nice work!