Well Mike - I see your message has gotten several views but no responses so it may be no one has done what you're attempting or maybe they don't understand what you're doing. I am going to try to help.
Your main question seems to be about the tensioner spring. My answer is "no" it's not as simple as changing to the other style tensioner spring. The spring style is determined based on the tensioner arm. I believe you saw these 2 tensioner springs on the CCS site:
Sorry for the different size images but that's the way they are shown.
The reason for the different springs is the 2 different tensioner arms which CCS shows as follows:
The top tensioner spring pic goes with the top tensioner arm pic. The bottom spring goes with the bottom arm.
I suppose your next question then becomes, can you just change the arm and spring and maybe get the correct alignment? I don't know if it would make any difference. I believe they both use the same mounting shoulder bolt and the alignment wouldn't be any different.
So, I don't know if that leaves you to going with red neck engineering or not. I don't know which way your alignment is off. If the tensioner pulley is "to low" on the deck I assume you already thought of just adding a washer where the shoulder bolt goes thru. If the tensioner pulley is "to high" then maybe you could consider adding a washer where the tensioner pulley mounts to the tensioner arm so it sits a little lower.
Will all this work in the end and last? That's a really big question. I never liked mixing and matching this stuff because of exactly what you are encountering. You might get it all fixed and then discover the belt covers don't fit correctly, or worse the deck doesn't cut and thro grass like it should.
I'm also wondering about you stating spindle assemblies from "32 inch" deck. That sounds like a Cadet deck (lawn tractor) or something and not the Cub Cadet (Garden tractor) deck. Maybe the 32" is a typo and you meant 38". In either case I'm wondering if you installed one of the 32" deck spindles on the 42" deck and checked the blade placement on the underneath side to see if it's at the same level as the original spindles. If the placement is different your deck may not operate well at all.
I hope this helps you out a little. Please let us know what you do to solve your problem.