MySQL - How can I speed up a 50+GB fixed width text file import for a 1000+ column table? (Can't remove columns)
MyISAM is probably as fast as InnoDB for this action.

I suggest you minimize the work during the LOAD and plan on doing TRIM, etc, after the data is loaded.  That is, load the data into a staging table; then perform various conversions as you copy the data to the real table; then drop the staging table.

This 'staging' can also give you an easy way of splitting up the columns into tables.  Or consolidating the columns into a single JSON string, or something else.

If you provide more details on the data and the transformations and the 1000+, I can be more specific.

More

Oh! Sounds like Punched cards.  Or mag tape..  I would


Read the text into a single column declared as TEXT.
Probably I would also have another column: id INT UNSIGNED AUTO_INCREMENT NOT NULL.
Meanwhile, I would generate SUBSTR(t, 12, 23) clauses based on what the split up needs to be.
And decide how to build the schema.  Are these medical records?  Animal characteristics?  Quiz results?  What?  Census data?
Are some of the "columns" repeated a lot?  For example for census data, I might expect the first two columns to be "state" and have about 51 distinct 2-character values, then the next ~20 columns be the county, with about 3000 distinct values, etc.  If so, then that definitely suggests a structure (states contain counties contain cities ...)
After deciding on the several tables to spread the data across, build SELECT queries to pull the data out and put them into the other tables.


Continuing with the example:

CREATE TABLE Cities (
    id MEDIUMINT UNSIGNED AUTO_INCREMENT NOT NULL,
    state CHAR(2) NOT NULL,
    county VARCHAR(20) NOT NULL,
    city VARCHAR(20) NOT NULL,
    PRIMARY KEY(id),
    INDEX(state, city)
) ENGINE=InnoDB  CHARACTER SET ascii;

INSERT INTO Cities (state, county, city)
    SELECT DISTINCT
            SUBSTR(t, 1, 2) AS state,
            SUBSTR(t, 3, 20) AS county,
            SUBSTR(t, 23, 20) AS city
        FROM Raw;


After that, it gets trickier, because you want to use cities.id in whatever table comes next, rather than repeating the state+county+city again and again.

Get the idea?  Want to share the type of data you have?

Sure it will take hours, probably even days.  But the structured result will be better than a nearly useless regurgitation of the raw data.

Also, think about how you want to eventually query (SELECT) the data.