I'm pretty familiar with that other forum and am myself committed to the stroker route though I'm not going to low-buck mine. I really did consider alot of options, weighed the pros and cons of each and settled on this as the best solution for me. I've re-geared to optimal gearing for my tire size and needs, done a series of bolt on mods and while it's all much better than the previous 21 years of ownership, found I still want more power specifically from 2000-4000 rpm so that I can safely pass on increasingly busy 2-lane mountain highways.
I would say there are some things that should be changed from Cheromaniac's recipe for a TJ. They are for an XJ (and an earlier one at that) and some things I don't think are mentioned.
#1 For a TJ, that cam is not optimal. Comp Cams has a cam for the thrust plate found in the TJ 4.0L motors and you'll want to go with one of those if you're going to stick with flat tappets. But the standard lift HO ones are out of stock atm. You might want the larger one anyways. If you care, I'll pull the cam numbers.
#2 You'll almost certainly need to have the donor block decked .030 -.050 to get proper quench to get good low rpm torque from higher compression and prevent pre-detonation. You need to have a good machine shop locally to do this and there are fewer and fewer around. You might also have issues with taper in your cyclinder bores from mileage and other issues that require it to be bored out a bit. You can just make the assumption that you need to go 0.030 over and have the machinist bore it out.
#3 Forged pistons are not be the best option for a NA motor. They have a different growth rate than hypereutectic pistons and tend to be noisier on cold start in a cast iron block (piston is rocking in the bore). Also Russ Potenger is in a semi-retired state these days and has been a bit hit or miss on speed of response and delivery, though people still like working with him. Clegg has good parts avialbility though and frankly good kits ready to go.
#4 Porting the head is still a good option, but you'll want the correct head for YOUR TJ, not the HO head in that list. The 0331 TUPY is prefered for later ones, but if you have a 0331 and it is not cracked by now, it's probably fine. And you probably want one of these as they support the coil rail. Also the Edelbrock Performer 4.0L head provides a bunch of advantages, but also has some disadvantages and has had some issues. You might consider it. It supports both coil rail and distributor systems.
#5 For alot of the early XJs, ODBI meant the computer could not be tuned. You do need the larger injectors to prevent going lean at WOT higher rpms, but with a TJ you can tune the engine with HPTuners. I believe all years of the TJ need an EV6 injector. There is some confusing terminology about impedance used in injectors, but EV6 is the correct type for a TJ and avoids the issue. To really get it dialed in on open loop, you'll want a wideband O2 sensor installed above the final catalytic converter in your system. Ideally you'd want it above pre-cats but it's not practical. You will likely need to adjust the basemap using WOT and the wideband in order to get startup idle, STFT and LTFT closer to target as well.
And finally, it's alot of work to do all of this, not have it dialed in properly and end up with some disappointing dyno results. Some people have seen as little as 40hp gain (but also realize the TJ has around 30% driveline losses). Yes you'll have more power with the Low buck option, but not as much as you probably expect for the amount of effort you put in. With a little more planning and work in the build these motors are able to reliably deliver 300hp, see a significant bump in low end torque and power and greatly improve drivability.
And I'd second
@Rickyd that intake and exhaust improvements still matter with the stroker.