Just a thought, but when you've had everything together and been able to start your truck in neutral, have you pushed the brake pedal and the clutch pedal at the same time? For some reason, my owner's manual says that the brake pedal has to be depressed before you shift into gear. The only thing I can think of is that since the brake booster takes vacuum, and the brake switch is activated, it allows, somehow, the engine to slow the RPMs up enough to where it's easier to engage in gear.
When I replaced my 2.3L, and I had the problem of not being able to get my truck into gear, it was only after finding out about the brake pedal needing to be depressed that my truck wouldn't move.
Lastly, when you have the truck in neutral, and it's started, can you shift in between first gear and reverse? That would be indicative that the slave cylinder isn't allowing the clutch to release. If you get grinding as you try and put it into gear, then it would be indicative of either the slave cylinder piston not acting from fluid pressure, as I've said before, or it could be that the throwout bearing isn't properly lubricated. For fixing the lubrication issue, put some high-temp grease on the inside of the throwout bearing, as well as on the face.
Lastly, the only other thing I'm finding it could be is that the clutch plate (disc) is either warped or damaged, which I'm thinking is that it's probably damaged or broken.