The power pulsing is a symptom of the ESC overheating. I think HPI build it in as an 'early warning' mechanism for their ESCs to stop people toasting them. My WK did exactly the same thing when I ran 19T + 9.9V through it. The motor, ESC and battery all got really hot and the ESC started power pulsing on WOT. Leave it 2 mins and it cools off and goes okay but mine ran for about 2 mins then started doing it again.
However, I was running the ESC way over it's specified limits. All I can think is the motors you are using are not correct, or the batter packs are running too high voltage?
Are you still running original spec motors and are you still using 7.2V packs?
If so then either the work you are making it do is overstressing it (I found grass does that sometimes) or there is a fault with the ESC that's causing it to overheat. The latter seems unlikely though as the whole system is getting hot so it's more likely overwork.
What type of terrain are you running on, are their any steep slopes or jumps? Are there any places it would seem to be bogging down?
I'd also recommend switching to Deans connectors. Tamiya plugs like the ones HPI use suck.