CREATE TABLE Y1 (time REAL, value REAL);
CREATE TABLE Y2 (time REAL, value REAL);
CREATE TABLE Y3 (time REAL, value REAL);
...

CREATE TABLE VARLIST (VarID INTEGER PRIMARY KEY, name TEXT UNIQUE NOT NULL);
INSERT INTO VARLIST VALUES(1, 'Y1');
INSERT INTO VARLIST VALUES(2, 'Y2');

...

CREATE TABLE TIMESTAMPS (timeID INTEGER PRIMARY KEY, time REAL);
CREATE TABLE DATAPOINTS (DataID INTEGER PRIMARY KEY, timeID INTEGER, VarID INTEGER, value REAL);

INSERT INTO TimeStamps(time)
SELECT time FROM Y1 UNION
SELECT time FROM Y2 UNION
SELECT time FROM Y3 UNION
SELECT time FROM Y4 UNION
SELECT time FROM Y5 UNION
SELECT time FROM Y6;

INSERT INTO DataPoints(timeID, VarID, value)
SELECT (SELECT timeID
        FROM TimeStamps
        WHERE time = all_Y.time),
       VarID,
       value
FROM (SELECT time, 1 AS VarID, value FROM Y1 UNION ALL
      SELECT time, 2,          value FROM Y2 UNION ALL
      SELECT time, 3,          value FROM Y3 UNION ALL
      SELECT time, 4,          value FROM Y4 UNION ALL
      SELECT time, 5,          value FROM Y5 UNION ALL
      SELECT time, 6,          value FROM Y6) AS all_Y;