Mine is a 4.0 I6 HO with manual transmission - exactly what I wanted. I don't know if there is any advantage, based on personal experience, between HO and non-HO versions since I've only ever driven the HO. I've heard that the HO motor is better, though. I definitely wanted a 6 cylinder. Although the 4 cylinder versions can generally be found more easily and cheaper, the difference in gas mileage is not that significant and the performance of the I6 is better. What I liked about mine when I was looking and bought, though, is that the 91' is the first year that came with fuel injection (as opposed to carbuerated) and was the last year to come with the CJ style sport bar. I knew to look for rust and mine is remarkably free of it. The only place I've found any of significance is the front center body mount, directly under the radiator. This is lucky, perhaps, since I didn't know then to check the frame under and around the shock mounts where they can collect water and mud. Personally, I like the 5 speed manual transmission but I have also heard some who like automatics - though most are driving newer jeep models. Mine has the AX-15 which isn't the smoothest transmission through all the gears but it works well. The AX-15 is known to have some issues but is better than the transmissions in earlier jeeps. My transmission has an internal slave, which I still know very little about other than that some newer models have an external slave that is easier to deal with if the tranny does develop some problems.
Things to look for when buying - cracked exhaust manifolds are extremely common and mine had a small leak that I could have continued to drive with for at least a while. I did replace it, though, at a cost of about $300 parts and doing the labor myself. This can be expensive if you have the dealer or mechanic do it. Axles and gearing may be important, depending on what you intend to do with your jeep and how big of tires you want to run. I did not know anything about this when I bought mine and sort of wish I did, though I'm not sure yet how much difference it would have made. Mine has stock 3.07:1 gearing which is only "ok". Put much more than 30" - 31" tires on and it's likely you'll want to re-gear. I think some of the later years and sub-models came with better gearing but, if you're going to go to 33"-35" tires (or larger) and do serious offroading, you'll still probably want to re-gear and/or swap out rear axles anyway. Older vehcles, including even the newest YJ's that are now 15 years old, are going to need parts replaced. I just replaced my entire cooling system (radiator, water pump, thermostat, hoses) at a cost of about $350-$400 - again, doing the labor myself. First thing I did when I bought it, too, was replace all the fluids, spark plugs/wires/distributor, air filter, throttle positioning sensor, and a few other small items. Most of my $$, so far have gone into making sure it runs reliably. The most expensive mods I've made, so far, are a 1" body lift and new front/rear bumpers. I also bought a new soft top for it.
I paid about $4500 for my jeep a year ago thinking all I wanted was a basic "beater" jeep just for exploring the desert and back-country. Since, I have easily put another couple thousand into it and want to do much more - suspension lift kit, bigger tires, new axles/gears, fender flares, rocker panels, winch, etc., to make it more capable and more bulletproof as I now want to get into doing more serious off-roading. I have also found that working on, improving, and modifying the jeep is almost as much fun as driving it - except when it comes to opening up the wallet.
These forums are great for learning about options, etc. You are lucky! I wish I'd found this site before I bought mine as I might have waited and spent a little more up front to get one that already had suspension/gearing and other options. Not sure it would have saved me a lot of money, though, but might've helped getting me where I want to go a little faster.