my flywheel will be a cherokee flywheel, and whatever size clutch will fit on there, and only for the time being, a clutch assembled with splines to fit an sr4, but only (ill repeat) until i get a T5 for the car.
It should be common knowledge that by removing the driveshaft and four bolts, your SR4 will slide out and a T5 will slide in. The existing clutch, fork, throwout bearing, and pilot bearing do not need to be disturbed. A SR4 and T5 input shaft is completely identical.
Its hard to tell, but I gather that you have four speed SR4 behind a 258 in a Spirit, and you want to stick a 4.0 in it and then eventually find a T5 later to install. It seems that you currently have the mechanical linkage that came with the Spirit. You've come to the right place. There is alot to learn first.
The "more readily available clutch cylinder" you need is the AMC Eagle clutch cylinder. Period. None other will work. When we install Jeep AX15s, NV3550s, and NSG370s we're forced to use the slave cylinder specific to the transmission we're using, however we must always use the original clutch master cylinder. Its the only one that will fit in the space between the brake booster and the fender wall. A Cherokee, Jeep, Subaru, pretty much every clutch cylinder ever made will not fit (I've tried). I happen to know that its the very same clutch cylinder used in four cylinder Spirits since I own one. Since you're sticking with a T5 you'll also need the AMC Eagle slave cylinder too.
The pedal in your Spirit is different than the Eagle pedal and you will need to modify your existing pedal to mate up to the hydraulic cylinder. Most of the pedal is identical, but the connection on the side looks different. You have a shaft going through a hole in your firewall that hooks to the side of your clutch linkage on a diagonal plate looking thing. The hydraulic pedals have a horizontal post instead of that plate. It shouldn't be too difficult to modify your existing pedal once you see the picture. If no one else posts it in the next week, and you're not a dink, I'll take a picture of my Spirit pedal in comparison to the Eagle pedal. In the Spirit I converted I simply popped in a spare Eagle pedal instead of bothering to modify my old one, so I still have it. Someone here at the nest might have a spare Eagle pedal for you to buy.
The mechanical linkage and Eagle slave cylinder share the same dimensions and bolt holes too, so you do not need to modify anything inside the bellhousing. Its literally as simple as removing the two bolts on your bellhousing, popping the old bar out of the way, and then bolting a slave cylinder into the exact same two bolts.
Your clutch and pressure plate from the Spirit is identical to those from the 4.0. All the Jeep manual transmissions have this in common. Make sure to bring the pilot bearing for the SR4 and T5 over to your 4.0. The pilot bearing for a T5 is different than the pilot bearings used in newer Jeep Cherokee manual transmissions even though the splines are the same. It is possible to put a 4.0 where your 258 used to be without buying anything at all.
You plan on using the 4.0 flywheel. Thats a good idea because the fuel injection wiring harness is designed to be used with a 4.0 starter. The starter must match the flywheel. A 4.0 starter will not work with a 258 flywheel and vice versa. Also the 4.0 flywheel has the correct notches for the Crankshaft Position Sensor. The problem is that a 4.0 flywheel is a quarter inch thinner than the 4.0 flywheel and you want to install a T5 behind it. You're kind of screwed. What you'll probably end up doing is using your old 258 flywheel and starter. The wires going to the starter in your 4.0 harness then will not be needed since you will retain all of your original solenoid and starter wiring to go with the 258 starter. This means that you will need a Hesco CPS relocating kit to run your fuel injection.
Its possible that when you bolt your SR4 stuff to the 4.0 with its 4.0 flywheel that the throwout fork will not notice the difference in thickness. Its also just as possible that it will work fine most of the time and slip some of the time. The first time I worked on my Spirit clutch it drove fine for about a month before beginning to slip. The difference between a 9 inch and a 10 inch clutch is even smaller and yet the mechanical linkage did not have enough adjustment to adapt. After the cost of a new clutch and the time it took to install, I'll never make that gamble again.
We Eagle guys get around buying a 300 dollar Hesco kit by getting the transmission that goes along with the 4.0. You might also have this option since 2WD versions of the AX15 exist. The AX15 is a great shifting 5 speed that is actually much stronger than a T5. If you use an AX15 you will also have to use the internal slave cylinder and pilot bearing specific to it. The pilot bearing input is a normal 3/16 double flare line that works perfectly with your new AMC Eagle clutch master cylinder. Avoid the AX5, that's the weaker version found behind four cylinder engines.
Another option might exist, but its just as expensive. Advance Adaptors sells a T5 bellhousing identical to the SR4 one you already have, except that has a hole for the 4.0 sensor. It seems the sensor might be able to return a useable signal to the computer if the Hall Sensor is aligned to the starting ring. I doubt this is true since the CPS notches on a 4.0 flywheel look alot different than the starting ring. If it is true than drilling your bellhousing and mounting the sensor to interact with the 258 flywheel might be plausible. In the end you'll likely bite the bullet and buy the Hesco kit like the rest of us.
Of course you now have the option of using 4.0 accessories or 258 accessories. The serpantine belt can be taken off and all of your original V belt stuff bolted on the 4.0 without affecting the fuel injection. I personally like the serpentine belt better, but have converted over to V belts before because the AC pumps are different. Yes it is true that you can retain your original exhaust manifold with the 4.0 if you don't bother adapting to the headers and welding in an 02 sensor bung. The 4.0 Oxygen sensor will fit in the exhaust manifold where the 258 oxygen sensor was.