Right, just install your transmission and have your shaft trimmed to suit your exact measurements.
Shortening a shaft is usually well under $100 if all components are in good shape and reuseable, and if any more it shouldn't be much. Don't be afraid to pay a little more and go to a driveshaft shop that can properly balance it too. Many shops will shorten but not all will/can balance after it's done.

Grigg

•1951 GMC 250 in the Project Journals
•1948 Chevrolet 6400 - Detroit Diesel 4-53T - Roadranger 10 speed overdrive - 4 wheel disc brakes
•1952 Chevrolet 3800 pickup
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"First, get a clear notion of what you desire to accomplish, and then in all probability you will succeed in doing it..." -Henry Maudslay-