Defining base frequency, multiplier and divisor for dynamic clock manager

Your design will not function correctly if it runs at 100 MHz but is only spec'd (by the tools) to run at 50 MHz. If it does, then it's a one-off miracle that wouldn't work when you make a change and rerun the tools. Don't do it. Don't even do it if your clock is 100 MHz and the tools tell you the design can run at 99.5 MHz.

To solve your problem you can either write a simple 'divide by power of 2' clock divider to reduce the clock frequency (something like this in Verilog):

reg [n:0] count; 

always @(posedge CLK_100) begin
  count <= count + 1;
end

BUFG bg_0 (.I(count[m]), .O(CLK_DIV));

(where 'm' <= 'n' and 'bufg' is a global clock buffer, and must be used for synchronous designs) or use a Digital Clock Manager (DCM).

Hopefully that solves your pipelining issues as well unless you absolutely have to run the entire design at 100 MHz. Other than pipelining you can consider using FIFOs if you have part of the design running at 50 MHz and the other at 100 MHz, but you'll have to say a bit more about what you're doing to get more meaningful help here.

A small micro would do this easily. You can set up a capture compare peripheral to count input pulses and read/clear at a regular interval (e.g. 50ms - use a timer interrupt for this)
Then write result (after multiplying by necessary value - e.g. in above example: capture_result * 20 = Hz) to whatever display you have in mind.

A non-micro solution could be produced with some discrete logic ICs, there are quite a few designs floating around on the web. It would be a pretty "old school" solution but may be fine for a one off home project (and cheap) Here is a 0-40MHz example (from this page)

For higher frequencies a small CPLD/FPGA would work well and would be a quick/easy HDL program to write - may be an idea if you have a small dev board lying around.

There are almost certainly dedicated ICs/Modules available if you have a look around. Most DMMs probably use an ASIC of some sort to provide multiple functions, though some of the cheaper models may use off the shelf stuff.