After creating a new $.$mas file with the adjusted code that was suggested by the expert it appears the problem is still persisting when I run through test cases. However now it appears to move to the CheckROT$13$ loop which is an improvement from being stuck in the main loop I had previously.

Here is the code as it stands currently. The aim is to have the program move to output after a single period $(\text{'}.\text{'})$ is entered.

$/$ Initialization

ORG $100$

$/$ Initialize Ptr $($pointer$)$

Load Start

Store Ptr

$/$ Main Program

MainLoop, Input $/$ Input a character

Store InVal $/$ Store input in InVal

Load InVal $/$ Load input value to AC

Subt ChPer $/$ Check if input is a period

Skipcond $400/$ If AC $==0($input is $\text{'}.\text{'}),$ jump to OutputStart

Jump CheckROT$13$

CheckROT$13,$ Jns ROT$13/$ Call ROT$13$ subroutine to transform the character

StoreI Ptr $/$ Store the transformed character in memory

Load Ptr $/$ Load pointer address

Add One $/$ Increment pointer

Store Ptr $/$ Store updated pointer

Jump MainLoop $/$ Repeat the input loop

$/$ Output Phase

OutputStart, Load Start $/$ Initialize pointer to the start of stored characters

Store Ptr

OutputLoop, LoadI Ptr $/$ Load the character from memory

Subt ChPer $/$ Check if the character is $\text{'}.\text{'}$

Skipcond $400/$ If AC $==0($character is $\text{'}.\text{'}),$ jump to EndProgram

Output $/$ Output the character

Load Ptr $/$ Load pointer address

Add One $/$ Increment pointer

Store Ptr $/$ Store updated pointer

Jump OutputLoop $/$ Repeat the output loop

EndProgram, Halt $/$ End the program

$/$ ROT$13$ Subroutine

ROT$13,$ HEX $0$

Load InVal

Add Val$13$

Store Hold

Subt ChZ

Skipcond $800$

Jump NoAdj

Add ChA

Jump Done

NoAdj, Load Hold

Done, JumpI ROT$13$

$/$ Constants

ChA, HEX $0041/$ Constant value $\text{'}$A$\text{'}$

ChZ$,$ HEX $005$A $/$ Constant value $\text{'}$Z$\text{'}$

ChPer, HEX $002$E $/$ Constant period char $\text{'}.\text{'}$

Val$13,$ DEC $13/$ Constant ROT$13$ value

One, HEX $1/$ Constant value $1$

Start, HEX $200/$ Constant address for starting memory location

$/$ Data Area

InVal, HEX $0/$ Subroutine input value

Hold, HEX $0/$ Temporary variable

Ptr$,$ HEX $0/$ Character pointer