There are two areas to pay particular attention to when you R/R the inner primary.
When installing the inner primary, it is real easy to nick the inner primary race oil seal on the trans main shaft when installing the inner primary. Suggest that you use duct tape or some other material to cover the trans shaft splines and protect the seal.
You didnt' say which model year and the later model years have the flanged bolts with the rubber seal under the flange to prevent outer primary lubricant from leaking through the bolt holes and leaking out between the inner primary and the motor case. Earlier models did not have these self sealing bolts and relied on RTV sealant behind the bolt and lock to seal against the chain case lubricant from seeping through and leaking. Some guys apply the RTV sealant between the inner primary and the motor case which is a bad idea and the MoCo has a tech bulletin advising against that approach. If you have an earlier model, application of some black RTV sealant between the lock and the primary and between the lock and bolt head will seal the inner primary. I use Hylomar sealant for this because it never takes a set. The three bolts behind the clutch are the worst offenders. If you have a later model, toss the old bolts and replace with new.
Both topics are covered in the manual but, IMHO, deserve special attention. It is very disheartening to R/R the complete primary, finish the task at hand and see that small spot of oil on the floor after the first 100 miles.