Understanding Unexplainable Bible Passages

Have you ever come across Scripture passages that don’t make sense?  The kind that church leaders could never explain to your satisfaction, or worse, they told you to ignore? Here are some that used to confound me (all from the Amplified Bible):

Hebrews 9:28: Even so it is that Christ, having been offered to take upon Himself and bear as a burden the sins of many once and once for all, will appear a second time, not to carry any burden of sin nor to deal with sin, but to bring to full salvation those who are [eagerly, constantly, and patiently] waiting for and expecting Him. (Emphasis mine)

What is this full and future salvation?  And why does it sound like it is only for those who are continually looking for Christ’s return? There were other unexplainable passages about it:

1 Peter 1:5: Who are being guarded (garrisoned) by God’s power through [your] faith [till you fully inherit that final] salvation that is ready to be revealed [for you] in the last time.

1 Peter 1:9: [At the same time] you receive the result (outcome, consummation) of your faith, the salvation of your souls.

These passages say that this future or final salvation is the salvation of our soul. How is it different from the salvation that we receive when we believe in Christ? Ephesians 2:8-9 tells us that salvation is a free gift based upon our faith in Christ and not upon our works, lest we should boast.

Then how do you explain James 2:14?:

What is the use (profit), my brethren, for anyone to profess to have faith if he has no [good] works [to show for it]? Can [such] faith save [his soul].

These passages did not make any sense until I understood the difference between present salvation (spirit salvation) and future salvation (soul salvation).  Chitwood explains the difference in this short tract.