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I've got a base 07 5 speed I changed the clutch flywheel, pilot bearing, slave cylinder etc, I cant seem to get the transmission flush with the engine block I always have about a 1/2 gap I've been at this for a few days. Any advice? Do I have to get it set and force it in with bolts because of the slave cylinder?

Edit: my clutch kit didnt come with a clutch alignment tool I tried a universal tool it didnt work out so I picked up dorman 14523 clutch tool and it fits pretty well only thing is it has slight wiggle room in the pilot bearing
Welcome to the forum.

The slave cylinder only pushes on the clutch when the pedal is depressed to disengage the clutch, so there should not normally be any force on it. I suspect you have an incorrect part, or a spacer that does not belong.
 
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I'm using a duralast clutch kit from autozone "oem replacement" I'm stuck I dont know what to do next to be honest.
I would compare each part to the ones you took out to see if something is different with one of them.

I assume that the pressure plate is screwed down tight against the flywheel, and the clutch disc is being held solidly.
 

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It is and its torqued down. I believe all the parts are the same but the new slave cylinder seems a little bit longer than the one that was in the car. I'm not 100% sure I'm going to go check all the parts later today
A longer slave cylinder would certainly cause this problem.
 

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The new "what" has a longer travel?
 

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Yes I did. And also yes I was referring to the slavecylinder/tob having a longer travel.
Could it be because my pilot is too far in the crank or too far out? The way it looks it's pretty much on the money but It might be off. I tried inserting the tranny without the clutch and pressure plate and it fit in there perfect. So I'm not sure
The slave cylinder seems to be the trouble spot. Assembling with everything but it would eliminate everything else.

Is the collapsed height of the new slave the same as the old one? And how much force does it take to collapse it compared to the force you are seeing in assembling the transmission to the engine?
 

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I tried installing the tranny without the slave and it still didnt go. But since then I readjusted the pilot and clutch so I'll try again. And yes the new slave collapsed is lower than the old one. I'm not sure how much more force it takes to collapse because I havent had a chance to work on the car for a few days. I'm going to get tomorrow to work on the car if I can get it done that'll be great if not I'm working for the whole week.
That pretty much points at clutch alignment. You may need a better clutch alignment tool.

I once was able to align a clutch using the transmission input shaft, but it took several tries, and I don't really recommend it:
  • Assemble the clutch t the flywheel, but do not tighten the pressure plate completely, leave it loose enough for the clutch to slide under it.
  • Install the transmission without the throwout assembly, and use it to shift the clutch into alignment. Do not force it into position.
  • Carefully remove the transmission to avoid pushing the clutch out of position.
  • Torque the pressure plate, install the throwout assembly, and reinstall the transmission.
  • Repeat as necessary when the clutch gets pushed out of alignment when pulling the transmission back off.
There really is no substitute for the proper alignment tool.
 

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Unfortunately I didnt get a chance to work on the car today, and wont be able to work on it for the whole week with Thanksgiving being around the corner. But with this extra "free time" I'm going to order a proper clutch alignment tool. (I still think its completely ridiculous that I didnt recieve one with my clutch kit, wasted over a week of free time) I've found this one Polaris Slingshot Parts

I'm going to order it if it's not the correct one please do let me know so I can cancel my order. And thank you very much for all the tips and advice gives me more confidence that I'll get the job finished.
That is the one that DDM says will fit, so I am pretty confident that it will.
 
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