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The input shaft swap is to the accommodate the the bell housing. It should have no influence on the starter.
If you have the engine and bellhousing already. attach the bell housing to the engine block (ensure the block plate is also used) measure the depth to the face of the pilot bearing and the depth of the hole (in the crank).
Then measure from the front of your T-5 the the step of the input shaft, and also the pilot section of the input shaft.
Keep in mind the diff in the two shafts length is .067" (not .067")
So a long shaft and short (new style) bellhousing the trans will not bolt up and will be approx .67 away from the bellhousing, likewise a short shaft and a longer bellhousing (94-95) the pilot shaft on the trans won't enter the pilot bearing in the crank.
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