The generation 2 trucks 94-01 (it might run back further, but I dont know much about pre94 trucks) have had some basic but common and important issues. One being the plenum, they used a crappy gasket and or too long of bolts. There is some argument on the exact cause, whether it be the steel pan on an aluminium intake (Not a huge problem) the thin crappy gasket (big part of the problem) and or too long of bolts (possibly a large part). This resulted in lots of crankcase vapors being drawn into the intake and bringing lots of oil with it. This as a result fouled out cylinders 7 and or 8 most commonly. The Hughes repair kit solves every possible reason as it provides an aluminium pan (expansion is still different between the cast intake and rolled pan), shorter bolts, and a better gasket (especially if you got the fel-pro gasket).
The death flash was, as I remember and have read in the TSBs, not a solution or fix for the plenum issue, but instead detonation, which CAN be aggravated by the plenum issue but not solely caused by the plenum issue. The "Deathflash" or factory authorised update, solves the problem of detonation by retarding ignition timing and fuel injection both, if memory serves. The result is noticeably less power and sluggish operation as you are losing valuable burn time due to the delayed ignition.
The solution is two fold, the plenum must be fixed, otherwise you'll foul out your cylinders and are likely to start detonating or 'kill' the cylinder. Then you must get the PCM programmed by someone like HemiFever, or FlyingRyan with an SCT tuner.
Since you have the plenum done already, the next step it to get it tuned. HemiFever is basic, you will see some gains, but its commonly accepted here that FlyinRyan has a better setup for his tunes. Either is going to cost at least $350, most likely you're looking at about $500 unless you get some deals on an SCT X3 unit. I'm sure HemiFever has some options, but I know FlyinRyan has different 'canned' tunes for different octane fuels, specific bolt on upgrades such as heads and cams, etc. However, as you're stock, you'd just get a stock tune, likely in whatever octane rating fuel you want to pay for.
I'm not sure who is cheaper between the two, but I am sure FlyinRyan has the support of most here on the forum.