You've caught me in a very busy week... so just briefly try this (I haven't fully checked all your code) and see if there's an improvement...

For the write...

For CounterA=0 to 98 step 2
Addr=CounterA
Data_In =Temp.LowByte ' Data_In is data TO EPPROM
Gosub EWrite
Addr=Addr+1
Data_In =Temp.HighByte ' Data_In is data TO EPPROM
Gosub EWrite
Temp =Temp + 1000 ' Add 1000 to the previous value
Next CounterA

For the read...

For CounterA=0 To 98 STEP 2 ' Create a loop of 50 WORD VALUES
Addr=CounterA
Gosub ERead ' Read the byte from the Eeprom
Temp2.LowByte= Data_Out
AddR=AddR+1
Gosub ERead
Temp2.HighByte = Data_Out
Next CounterA

1. It's dangerous to manually advance the counter variable in a for-next loop, because when it steps, it'll step from your new altered value.

2. Doesn't counting "From 0 to 100 step 2" produce 51 steps (not 50)? Since 0 is the first step, and 100 is the 51st step?