Know how to check for codes? Any codes being thrown out?
The Howell systems are fairly simple: fuel delivery or electrical problems.
How long have you had the Howell installed, and did you do the install yourself? Where is your pump currently? Like dmock, mine is just tucked under the transmission cross-member.
I guess I'd try ruling out one thing at a time - fuel delivery is probably a good choice. Your pump could be going bad, your filter could be full of garbage, or like BW said - it could be vapor lock. I don't think the Howell system is as prone to lock as the original system, but your symptoms remind me of them. Make sure your fuel return line is unobstructed by forcing air through it and listening for bubbles in the tank.
If it's not fuel delivery, on to electrical. Check all your grounds and consider the relays. I had a problem with my relay harness right off the bat and had to crimp it down to make proper contacts with the relay. Check for codes as I mentioned.
Other than that - make sure all your bolts are tight on the intake/exhaust manifolds and throttle body. Loose connections make for oxygen leaks which can throw off the system.
Good luck, let us know what you find!