I would also choose the short shaft most of the time as it is a bit more desirable to other people if you were to change something in the future and wanted to sell it. In a pickup it doesn't matter as much, to me anyway.

One variable to consider is the driveshaft length. I will usually get a used driveshaft from the junk yard and shorten it. I prefer the one piece shaft and the common lengths (cheap) might not be long enough to reach the short shaft trans, especially if you have a long bed. You might source the driveshaft and rearend before you pick the trans since you have a choice. As for which model of vehicle to source the shaft from, look for a 73 - 82ish chevy pickup, right before they put the OD in them. The splines and driveshaft yoke for a TH700R4 are the same as the TH350, but the 700R4 is longer by a couple inches. So, the longest stock driveshaft that I have found was out of a late 70’s long bed GM pickup.
Hope this helps,

jason

1937 GMC T16 468 BBC th350, 4.10
1941 Dodge COE 5.9 cummins, 9 speed roadranger
1947 Diamond T COE, hercules and 4 spd, all original
1955 Chevy LCF 9.0L IH diesel AT545
1962 Corvair (Elsie)
1967 Jeepster Commando
1968 K10
1970 Chevy C50 box truck