As has been mentioned to you several times, you do not have Excel files. You have TEXT files, so please stop calling them Excel files. The method for handling Excel files is completely different from the method for handling TEXT files. People may start thinking you want to use Excel files and start giving you suggestions that don't help you.
The first issue you are having with the extra rows is due to the Write to Spreadsheet File VI. It adds an extra line due to the Array to Spreadsheet String function that it uses internally. To get around this you would need to basicall make your own version of the Write to Spreadsheet File that removes the extra line before writing it to file. This is easier than it soundsas you can simply copy the code it has and just add a Match Pattern right after the Array to Spreadsheet String to look for the newline at the end of the string and take the stuff before it.
As for the second issue: since you are dealing with TEXT files you have to look at this as if the file I/O were a firehose. The only way to go back into the flow is to move the file pointer. You have to do this yourself - the function will not do that for you.