Mini-mill First Timer.. Tram Troubles..

When you are framing the head to the table the indicator should be almost level with the table. You can also use a page taken from glossy magazine across the table to prevent the indicator dropping into the slots.
 
Your tools are fine. Sometimes it's not so much the tools, but the tramming sequence itself on the new mini mill owners that cause folks issues. FWIW here's what I learned as far as tramming/checking alignment.

First tram/adjust the head to align the spindle to the column.

I mount the indicator base on the column and the indicator against the side and then front or rear of a 6 to 7" piece of 1/2" drill rod mounted in the spindle/collet. Rotate the spindle by hand and get the middle average. Do this at the bottom and top of the drill rod (on both a side to check Y alignment, and front or back to check X alignment) and check for deviation and adjust/shim as necessary. If this is out of alignment I would also check clean the surfaces well and look for any nicks on the mating surfaces or debris that can cause issues. Especially if you've had it off. These alignments are usually on or very close, but you can add shims (foil or whatever) where your head mounts to the column to adjust.

When the prior step is complete and aligned next tram the spindle to the table by adjusting the column at the base using shims if necessary.

I mount the indicator to the spindle/collett (on an "L" or upside down "T" setup) and the indicator at/against the table. Swing/Rotate the indicator front to back of the table to check "Y" alignment and then left to right to check the "X". Shim where the column mounts to the base if needed.

From then on re-tramming can normally be done by aligning the spindle/head to the table in the event you needed to rotate the head (if yours rotates) or you crash into something. Keep in mind that if your head/spindle is not aligned with the column, just aligning the spindle to the table is not going to tram your mill properly.
Don't tram your mill off your vice. Tram using your table in the second step. When the spindle to column and spindle to table is all trammed and everything looks good, then you can mount your vice and "align" it square with your table/spindle. Hope all that makes sense and I didn't confuse the issue and complicate things...
 
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