The 3rd gens actually never came with SE and GXE badges. The 89-94 GXE's had the VG30E, all were automatic, I believe they always had body colored mirrors and had chrome accents like on the grill, tails, and around the windows.
I believe all SE's had a wing and fog lights, mirrors were black instead of body colored (at least on the 89-91's, not sure about the 92-94), they were available with an auto or manual. 89-91 had the VG30E, 92-94 had the VE30DE. 92-94's had the option for a viscous limited slip differential. If you're looking to swap to a manual the 92-94 5-speed with VSLD is the way to go. They're slightly stronger than the previous ones.
Sounds like you probably have the VG30E. Looking at the engine, its SOHC and the intake manifold comes forward with twin throttle bodies. The VE30DE is DOHC with the throttle body pointing to the driver's side.
The VG30E is definitely low on power stock but an incredible engine as far as reliability and power potential go... they absolutely love boost. You really don't even need to change the internals if you go with some boost. There are numerous VG's out there pushing 400+ hp on stock internals. I know of at least one or two pushing over 500 and I believe the highest seen on stock internals is around 700, though it likely didn't last to long making that much. Tons of 300 and 400 hp stock block VG's out there being daily driven though.
The big thing you have to worry about is the transmission. They are weak... very weak. Like I said above, the 92-94 5-speed is the way to go but it still has its issues. The input shaft bearing is the weakest spot in these. There's a company on the east coast called Import Performance Transmissions that knows of the issue and can put in a larger bearing, which should fix that problem permanently. If you're looking for a lot of power you may look into cryo treating the gears as well. Third is usually the most problematic when it comes to power as its usually the smallest in there.
If you have the VG30E my recommendation is to keep the stock engine in there and do a custom turbo setup from there. If you want to use salvage yard parts you can make a decent turbo setup with Z31 or 2nd gen Maxima manifolds. I recommend using two right/rear manifolds and making a custom crossover pipe to mount the turbo on. You'll have to relocate the battery to the trunk but this gives you a good deal of room for large turbo upgrades down the road.
Intake manifold wise I really like the 2nd gen Maxima's manifold. It should flow the best next to the Pathfinder manifold, which won't fit under the hood. There is also a company out there that can modify the 2nd gen manifold to flow much better than stock. I think they may even sell some on ebay.
If you go the 2nd gen manifold route I highly recommend going to top feed injectors. I believe the 2nd gen uses top feeds but if not you can go with a 84-86 300ZX lower intake manifold and fuel rail with the 2nd gen upper manifold. From there you can use large injectors like from the RX-7's (440's and 550's are common, larger available) and the 1975 Mercedes 450SEL 420's are popular as well. With our ECU you'll want to get high impedance injectors just so everything works smoothly. I think some guys run resistors on low impedance injectors but I'm too lazy for that.
Another nice thing about going with the top feeds is there is going to be a very nice fuel rail coming out soon for the VG's with top feeds. The stock rail should flow plenty of fuel but if you want to go all out, I believe the ones they've done so far can flow enough fuel for 700-ish hp.
There are quite a few cam options out there as well. Cams are said to make pretty big differences in the VG. The best route to go would be a custom grind in my opinion. Most pre-made cams out there are made to work in both normally aspirated and turbo setups, which means is not optimized for either. You can go to a company like Isky or similar and tell them what you're doing to it and they should be able to get you a grind that matches well with your setup.
Ferrea offers 1mm oversized valves as well, but I don't think many people really use them. A good port and polish will help. There are also adjustable cam gears out there that is a good mod to fine tune your timing.
As far as tuning goes you have quite a few good options. Probably the best out there is using a romulator with a program like Nistune. It pretty much turns your ECU into a stand alone unit, a very powerful setup.
I believe one of the 300ZX ECU setups from Ash-Spec is said to work perfectly with the VG Maxima ECU. Its pretty much the same setup as the romulator really.
You also have you piggy back units like the Apex'i S-AFC but if you're looking for a decent amount of power these won't offer enough control. I think the Greddy E-manage is a better unit as far as control goes... but with the romulator options out there for our ECU's the piggy backs are a bit expensive.
You also have the option of going with Jim Wolf Technology. Its expensive but they can program the ECU for you to the specs you need. They won't be able to get it quite as perfected as if you were to go with the romulator setup but its not a bad option if you aren't into the ECU programming.
If you have the VE30DE everything will be a little more custom. They had some variable valve timing issues, which caused the engine to clack really bad when they went out... the thing would literally sound like a diesel. You can rebuild the VTC units so that they work properly and don't make noise. If you do, be sure to use a high quality oil filter as that is generally accepted as the reason why they die.
The VE hasn't really been modified all that much but I believe its an excellent engine to put some boost to. Its basically a compact version of the VG30DE in the 300ZX. It has a forged crank with 8-bolt flywheel flange. Rods are the same as the VG, pistons can be swapped from a VG which means you can get some low compression VG30DETT pistons for some extreme boost if you wanted to.
The turbo setup would have to be completely custom though. The manifolds from the VG won't bolt up that I know of so you'd have to make your own manifolds for the turbo. As far as ECU tuning its a little more difficult not having the EPROM style ECU like the VG but there is a guy working on getting one of the 300ZX computer setups to work with the VE as the two ECU's are very similar. JWT can also do VE ECU's I believe so that's another option.
Hopefully that will give you a bit of a start. For some extremely good VG info take a look at
http://www.redz31.com. Its for the Z31 300ZX but it will all be the same. If you have any questions just let me know and I'll help out the best I can.